Jim Hayward, Ph.D., Sc.D., CEOGateway Conference, September, 2016

Nasdaq: APDN

Forward-Looking Statements

The statements made by Applied DNA Sciences, Inc. (the “Company”, or “us”) herein regarding the Company and itsbusiness may be forward-looking in nature and are made pursuant to the safe harbor provisions of the PrivateSecurities Litigation Reform Act of 1995. Forward-looking statements describe the Company’s futureplans, projections, strategies and expectations, including statements regarding future results of operations andfinancial position, business strategy, prospective products, timing and likelihood of success, and objectives ofmanagement for future operations, and are based on certain assumptions and involve a number of risks anduncertainties, many of which are beyond the control of the Company, including, but not limited to, the risks detailed inthe Company’s Registration Statement on Form S-3 (including Prospectus Supplements and any documentsincorporated by reference therein, including the Company’s Annual Report on Form 10-K for the year endedSeptember 30, 2015), and other reports filed by the Company with the Securities and Exchange Commission. Forward-looking statements include all statements which are not historical facts, and can generally be identified by terms suchas anticipates, believes, could, estimates, intends, may, plans, projects, should, will, would, or the negative of thoseterms and similar expressions.

Because forward-looking statements are inherently subject to risks and uncertainties, some of which cannot bepredicted or quantified and may be beyond the Company’s control, you should not rely on these statements aspredictions of future events. Actual results could differ materially from those projected due to our short operatinghistory, history of losses, lack of market acceptance of our products and services, market competition, changes in thelocal and national economies, and various other factors. All forward-looking statements contained herein speak onlyas of the date hereof, and the Company undertakes no obligation to update any forward-looking statements, whetherto reflect new information, events or circumstances after the date hereof or otherwise.

Focusing on the

mission.

Delivering the best

outcome.

DNA makes it

possible.

Helping the Defense

Logistics Agency secure

its electronic microcircuit

supply chain.

Over 700 thousand

components marked.

FSC 5330 FSC 5961

FSG 47

FSC 2530

FSC 2915

FSC 3110

Just completed: 2

federal

development

contracts.• OSD - extends DNA

marking to 66

additional Federal

Supply Classes

(>140 mm items

purchased/yr)

• MDA - high-volume

marking of

semiconductors

(FSC 5961 and

5962)

Cash and valuables

safely transported.

DNA makes it

possible.

The use of DNA-marked

degradation dye, and now

DNA-cyanoacrylate in the UK

has resulted in a 75%

reduction in cash transport

attacks.

105 Convictions

494 Sentence Years

Pushing it to the

limit.

Braking hard and

late.

DNA makes it

possible.

Ensuring the use of

authentic critical

components in

vehicles, commercial

aircraft and machinery.

That new prescription

is having a positive

impact on your life.

DNA makes it

possible.

Preserving patient safety

and benefit by ensuring

drug authenticity and

active ingredient integrity.

Target dumps supplier it says delivered fake Egyptian-cotton sheets

August 19, 2016

• Cotton Egypt Association estimates that 90% of products labeled Egyptian cotton” are fake

The joy of sleeping

in cool cotton comfort.

DNA makes it

possible.

Restoring integrity to the

worldwide

cotton textile supply chain.

Ensuring quality, comfort and

compliance.

100 million pounds of cotton

marked.

• After SigNature T DNA Marking Pima compliance about 100%

• Before SigNature T DNA Marking Pima compliance less than 30%

The Data Speak for Themselves

Applied DNA Sciences Expands US Cotton Tagging Business With Launch of New “HomeGrown Lonestar™” Program and Order to

Mark 50 Million Pounds of Cotton

SigNature® T DNA-tagging of Plains Varietal Upland cotton fibers to assure “Cotton Proudly Grown in the USA” label claim for textile quality and purity

throughout supply chain

STONY BROOK, N.Y.(September 7, 2016) —Applied DNA Sciences (Applied DNA), Inc. (NASDAQ:

APDN), a provider of DNA-based supply chain, anti-counterfeiting, authentication,genotyping and anti-theft technologies, expanded its US cotton tagging business by 50 million pounds as part of its newly

launched HomeGrown Lonestar™ program within the 2016 US cotton harvest. The cotton varietal

tagged as Lonestar comes from the famous cotton territories of West Texas. Applied DNA received an order for SigNature T DNA adequate to mark 50 million pounds of Lonestar cotton that is expected to ship before the end of September.

First launched in 2015, “HomeGrown™ — Cotton Proudly Grown in the USA” uses the Applied DNA botanical SigNature® T DNA to tag and test the long staple cotton fibers known as Upland cotton.

Upland cotton is the most widely planted species of cotton in the United States, accounting for at least

97% of all cotton production, or roughly 7 billion pounds per year.

The Lonestar program is a new addition to existing programs that apply SigNature T DNA to Pima

(known as PimaCott®, and to HomeGrown Upland programs that previously included Acala and Delta

cottons. The three DNA-tagged types of HomeGrown Upland cotton now provide the full spectrum of variety required by cotton manufacturers. Adoption has already begun with merchants,

ginners,manufacturers and retailers in India, Pakistan, Bangladesh, China, Turkey and the US.

“Given the global ambiguities in cotton sourcing, the demand for US cotton is getting stronger,” said Dr. James Hayward, CEO of APDN. “We have proved that if you can tag cotton fibers before they leave the

country, you can protect an entire supply chain. Sustainability and responsibility, in truth, begin at home. We believe that proof of origin for 100% of source cotton is the best way to exclude ethically-

challenged cottons, that either misrepresent origin or quality, or worse, may benefit from human

trafficking.” With the launch of HomeGrown Lonestar cotton, SigNature T DNA tags now provide full end-to-end traceability from the West Texas Plains to the retail shelf. Secure supply chain custody protocols,

storage, sampling and testing procedures are required as part of the Pimacott and HomeGrown programs, enabling retailers and brands to be confident in the label claims they make on the products

they sell to consumers.

About Applied DNA Sciences We make life real and safe by providing botanical-DNA based security and authentication

solutions and services that can help protect products, brands, entire supply chains, and

intellectual property of companies, governments and consumers from theft, counterfeiting,

fraud and diversion. Our patented DNA-based solutions can be used to identify, tag, track,

and trace products, to help assure authenticity, traceability and quality of products.

SigNature® DNA describes the platform ingredient that is at the heart of a family of

Increasing Demand for DNA-tagged CottonVolume and Variety

Pima

20

40

60

80

100

2014 2015 2016 Outlook as of 7 Sept

Pima

Lbs (milions) ofDNA-taggedCotton(to be)produced

Delta

Lonestar

Pima

Delta

120

Acala

Feeling confident that your

new ensemble was

ethically sourced.

DNA makes it possible.

Using DNA markers to verify

manufacturing locations, material

sources and product provenance.

August 4, 2016 Tweet from ILRF

At the US Chamber of Commerce

Cotton Certainty. Peace of Mind.

Determine if fiber is Pima, upland, or a blend with a patented diagnostic assay.

Tag cotton at the source with botanical-based molecular DNA to trace origin.

Forensically identify the geographic origin of cotton. Assay currently in development.

Never considering

your

shoes during a

marathon.

DNA makes it

possible.

Using specially-

engineered markers to

protect the integrity of the

synthetic fiber textile

supply chain.

digitalDNA® platform to support our

Customers

Business advantage: Transaction and information hub for textiles supply

chains, compliance agencies, and consumers.

Technology Platform Architecture

Spectral profile/

image

validation

Bar code data

entry - overt and

covert

RFID data entry Documents/

Images storage

DNA authentication

DNA Registry Extends to Supply Chain

Traceability

Supply Chain

• ADNAS produced and shipped

DNA

• SAS produced and shipped

gaskets

• ActionPak receive, IUID bag &

tag, ship

• DLA receive, validate and

authenticate

• Supply Chain reporting

digitalDNA® payoff for the ConsumerPimaCott™ proof positive…

Financial Highlights

$350 $520 $969 $1,855 $2,036

$2,721

$9,088

0

2500

5000

7500

10000

FY2009 FY2010 FY2011 FY2012 FY2013 FY2014 FY2015

$ I n

Th

ou

san

ds

Annual Revenue

0%

75%

150%

225%

300%

FY2013 FY2014 FY2015

Year over year revenue growth

-1738-1223

-479

213

-2246-2791 -2591

-3750

-2813

-1875

-938

0

938

Q1' FY15 Q2' FY15 Q3' FY15 Q4'FY15 Q1'FY16 Q2'FY16 Q3'FY16

Quarterly Adjusted EBITDA

Comparative Consolidated Statement of OperationsThree Month Period Ended Nine Month Period Ended

June 30, Variance June 30, Variance

2016 2015 $ % 2016 2015 $ %

Revenues $652,896 $2,267,671 $(1,614,7

75)

-71% $$2,550,332 $5,028,234 $(2,477,902) -49

Cost of revenues 121,260 129,016 (7,756) -6% 304,611 129,015 175,596 136%

Operating Expenses

Selling, general &

administrative

2,707,420 3,222,691 (515,271) -16% 8,616,246 10,323,809 (1,707,563) -17%

Research & Development 1,077,916 466,841 611,075 131% 2,861,583 1,587,326 1,274,257 80%

Depreciation & amortization 168,641 121,339 47,302 39% 557,968 354,144 203,824 58%

Total operating expenses 3,953,977 3,810,871 143,106 4% 12,035,797 12,265,279 (229,482) -2%

LOSS FROM

OPERATIONS

(3,422,341) (1,672,216) 1,750,125 105% (9,790,076) (7,366,060) 2,424,016 33%

Other income (expense) 55,330 1,334 (53,996) 4,048% 29,173 (4,019,042) (4,048,215) -101%

NET LOSS $(3,367,011) $(1,670,882) 1,696,129 102% $(9,760,903) $(11,385,102) (1,624,199) -14%

Use of Non-GAAP Financial MeasuresThis presentation includes Adjusted EBITDA, which is a non-GAAP financial measure as defined under Regulation Gpromulgated by the Securities and Exchange Commission. Generally, a non-GAAP financial measure is a numericalmeasure of a company’s historical or future performance, financial position, or cash flows that either excludes orincludes amounts that are not normally excluded or included in the most directly comparable measure calculated andpresented in accordance with GAAP. The presentation of this non-GAAP financial information is not intended to beconsidered in isolation or as a substitute for, or superior to, the financial information prepared in presented inaccordance with GAAP. Adjusted EBITDA has limitations as an analytical tool. Among other things, Adjusted EBITDA doesnot include all items of income and expense that affect the Company’s operations. Other companies may calculatesimilarly titled financial measures differently than does the Company.

We use this non-GAAP financial measure for internal financial and operational decision making purposes and as a meansto evaluate period-to-period comparisons of the performance and results of operations of our core business. Ourmanagement believes that these non-GAAP financial measures provide meaningful supplemental information regardingthe performance of our business by excluding non-cash expenses that may not be indicative of our recurring operatingresults. We believe this non-GAAP financial measure is useful to investors as they allow for greater transparency withrespect to key metrics used by management in its financial and operational decision making.

“Adjusted EBITDA” is defined as EBITDA adjusted to exclude (i) change in fair value of warrant liability, (ii) the loss onconversion of promissory notes, (iii) stock-based compensation and (iv) other non-cash expenses. “EBITDA” is defined asearnings (loss) before interest expense, income tax expense and depreciation and amortization expense.

Calculation and Reconciliation of Consolidated Adjusted EBITDAThree Month Period Ended

June 30,

Three Month Period Ended

March 31,

Nine Month Period Ended

June 30,

2016 2015 % 2015 % 2016 2015 %

Net loss $(3,367,011) $(1,670,882) $(3,467,623) $(9,760,903) $(11,385,102)

Interest expense (income),

net(2,660) (5,052) (4,062) (9,567) 26,807

Depreciation & amortization 168,641 121,339 170,981 557,968 354,144

(Gain) loss on change in fair

value of warrant liability- - - - - 2,994,540

Stock based compensation

expense525,186 1,057,097 499,668 1,522,304 3,595,631

Loss on conversion of

promissory notes- - - -

980,842

Bad debt expense 83,934 18,971 10,000 106,247 21,750

Total non-cash items 775,101 1,192,355 676,587 2,176,952 7,973,714

Consolidated Adjusted

EBITDA (loss)$(2,591,910) $(478,527) 442% $(2,791,036) -7% $(7,583,951) $(3,411,388) 122%

Clean Balance Sheet

($ in millions) As of June 30, 2016

Cash & Equivalents $7.1

PP&E $0.805

Other Current and Non-Current

Assets$6.3

Accounts Payable and accrued

expenses$2.2

Other Current and Non-Current

Liabilities$0.849

Stockholders’ Equity $12.2