The Collaborative International Dictionary of English v.0.48:

Indigenous \In*dig"e*nous\, a. [L. indigenus, indigena, fr. OL.
   indu (fr. in in) + the root of L. gignere to beget, bear. See
   In, and Gender.]
   [1913 Webster]
   1. Native; produced, growing, or living, naturally in a
      country or climate; not exotic; not imported.
      [1913 Webster]

            Negroes were all transported from Africa and are not
            indigenous or proper natives of America. --Sir T.
                                                  Browne.
      [1913 Webster]

            In America, cotton, being indigenous, is cheap.
                                                  --Lion Playas.
      [1913 Webster]

   2. Native; inherent; innate.
      [1913 Webster]

            Joy and hope are emotions indigenous to the human
            mind.                                 --I. Taylor.
      [1913 Webster]

WordNet (r) 3.0 (2006):

indigenous
    adj 1: originating where it is found; "the autochthonal fauna of
           Australia includes the kangaroo"; "autochthonous rocks
           and people and folktales"; "endemic folkways"; "the Ainu
           are indigenous to the northernmost islands of Japan"
           [syn: autochthonal, autochthonic, autochthonous,
           endemic, indigenous]

Moby Thesaurus II by Grady Ward, 1.0:

40 Moby Thesaurus words for "indigenous":
   aboriginal, atavistic, autochthonous, bodily, born, coeval,
   congenital, connatal, connate, connatural, constitutional, endemic,
   genetic, hereditary, homebred, homegrown, in the blood, inborn,
   inbred, incarnate, inherent, inherited, innate, instinctive,
   instinctual, local, natal, native, native to, native-born, natural,
   natural to, organic, original, physical, primal, primitive,
   temperamental, unacquired, vernacular