The Collaborative International Dictionary of English v.0.48:

underlying \un`der*ly"ing\, a.
   1. Lying under or beneath; as, the underlying strata of a
      locality.
      [1913 Webster]

   2. Hence: Fundamental; basic; as, underlying principles;
      underlying causes.
      [1913 Webster +PJC]

   3. Implicit; not immediately obvious; requiring careful
      scrutiny to discover; as, the underlying sarcasm in her
      seemingly innocuous remark..
      [PJC]

WordNet (r) 3.0 (2006):

underlying
    adj 1: in the nature of something though not readily apparent;
           "shortcomings inherent in our approach"; "an underlying
           meaning" [syn: implicit in(p), inherent,
           underlying]
    2: located beneath or below
    3: being or involving basic facts or principles; "the
       fundamental laws of the universe"; "a fundamental
       incomatibility between them"; "these rudimentary truths";
       "underlying principles" [syn: fundamental, rudimentary,
       underlying]

Moby Thesaurus II by Grady Ward, 1.0:

53 Moby Thesaurus words for "underlying":
   ab ovo, basal, basic, basilar, between the lines, bottom, cardinal,
   constituent, constitutive, covert, critical, crucial, cryptic,
   delitescent, dormant, elemental, elementary, esoteric, essential,
   foundational, fundamental, gut, hibernating, hidden, indispensable,
   latent, lurking, material, muffled, mystic, necessary, needful,
   obfuscated, obscured, occult, of the essence, original, possible,
   potential, primal, primary, primitive, radical, rudimentary,
   sleeping, submerged, substantial, substantive, under the surface,
   unmanifested, veiled, virtual, vital