Washington, D.C. 20549

                                   FORM 12b-25

                        Commission File Number: 002-78682

                           NOTIFICATION OF LATE FILING

|X| Form 10-K     |_| Form 20-F     |_| Form 11-K
|_| Form 10-Q     |_| Form 10-D     |_| Form N-SAR

For Period Ended: September 30, 2006

|_| Transition Report on Form 10-K
|_| Transition Report on Form 20-F
|_| Transition Report on Form 11-k
|_| Transition Report on Form 10-Q
|_| Transition Report on Form N-SAR

For the Transition Period Ended:__________________

Nothing  in this  form  shall be  construed  to imply  that the  Commission  has
verified any information contained herein.

If the notification  relates to a portion of the filing checked above,  identify
the item(s) to which the notification relates:



Applied DNA Sciences, Inc.
Full name of registrant

Former name if applicable

25 Health Sciences Drive, Suite 113
Address of principal executive office

Stony Brook, New York 11790
City, state and zip code

PART II - RULE 12b-25 (b) AND (c)

If the subject report could not be filed without  unreasonable effort or expense
and the registrant seeks relief pursuant to Rule 12b-25(b), the following should
be completed. (Check box if appropriate)

    | (a) The reasons  described in  reasonable  detail in Part III of this form
    | could not be eliminated without unreasonable effort or expense;
    | (b) The subject annual report,  semi-annual  report,  transition report on
    | Form 10-K,  Form 20-F,  Form 11-K,  Form N-SAR or Form  N-CSR,  or portion
    | thereof,  will be filed on or before the fifteenth  calendar day following
[X] | the  prescribed  due date; or the subject  quarterly  report or transition
    | report on Form  10-Q or  subject  distribution  report  on Form  10-D,  or
    | portion  thereof,  will be filed  on or  before  the  fifth  calendar  day
    | following the prescribed due date; and
    | (c) The accountant's statement or other exhibit required by Rule 12b-25(c)
    | has been attached if applicable.


State below in reasonable  detail the reasons why Forms 10-K,  20-F, 11-K, 10-Q,
10-D, N-SAR,  N-CSR, or the transition report, or portion thereof,  could not be
filed within the prescribed time period.

      Applied DNA Sciences,  Inc. (the "Company") is filing this Notification of
Late Filing on Form 12b-25 with respect to the  Company's  Annual Report on Form
10-KSB for the year ended September 30, 2006 (the "Form 10-KSB"). The Company is
unable,  without  unreasonable  effort and expense, to file the Form 10-KSB on a
timely  basis  due  to  unforeseen  delays  in  the  collection  and  review  of
information  and the  completion  of drafting the  necessary  responses to items
required to be included in the Form 10-KSB.

      The Company is currently  working with its independent  registered  public
accounting  firm to finalize the audit of its financial  statements for the year
ended  September 30, 2006.  The Company  expects that these  activities  will be
completed and the Form 10-KSB will be filed no later than January 16, 2007.


(1)  Name  and  telephone  number  of  person  to  contact  in  regard  to  this

  James A. Hayward                     (631)                    444-6862
  ----------------                   -----------            ------------------
       (Name)                        (Area Code)            (Telephone Number)

(2) Have all other  periodic  reports  required under Section 13 or 15(d) of the
Securities  Exchange Act of 1934 or Section 30 of the Investment  Company Act of
1940  during  the  preceding  12  months  or for such  shorter  period  that the
registrant was required to file such report(s) been filed?  If the answer is no,
identify report(s).

                            |X| Yes           |_| No

(3) Is it anticipated that any significant  change in results of operations from
the  corresponding  period for the last  fiscal  year will be  reflected  by the
earnings statements to be included in the subject report or portion thereof?

                            |_| Yes           |X| No

If so, attach an explanation of the  anticipated  change,  both  narratively and
quantitatively, and, if appropriate, state the reasons why a reasonable estimate
of the results cannot be made.

                           Applied DNA Sciences, Inc.

has  caused  this  notification  to be signed on its  behalf by the  undersigned
thereunto duly authorized.

Dated: January 3, 2007                      By:  /s/ JAMES A. HAYWARD
                                                     James A. Hayward
                                                     Chief Executive Officer