Why some species exhibit remarkable variation among populations while closely related species are relatively uniform remains unclear. The strawberry dart-poison frog (Dendrobates pumillo) exhibits spectacular color and pattern polmorphism among populations in the Bocas del Toro archipelago of Panama. In contrast, two other sympatric species of dart-poison frog, Phyllobates lugubris and Minyobates sp., show little color or pattern variation among island populations. Here we demonstrate that the color and pattern variation among populations of D. pumilio is not matched by higher levels of mitochondrial DNA sequence divergence relative to P. lugubris or Minyobates sp. Thus, neutral divergence in allopatry is unlikely to have caused the geographical differences observed in D. pumilio. We suggest that strong sexual selection associated with female parental care in D. pumilio, which contrasts the male parental care of P. lugubris and Minyobates sp., may have driven divergence in coloration and pattern in D. pumilio.