Three pupfish (Cyprinodon) morphotypes (two endemic) occur in some of the young (6000 ypb) saline lakes on the Bahamian island of San Salvador. The ‘normal’ morph, a detritivore/omnivore, is not different in its general features from Cyprinodon variegatus from other Bahamian islands. ‘Bulldog’ is a scale-eater/piscivore that preys upon normal pupfish, and ‘bozo’ is a specialized molluskivore. Reproductive isolation among these morphs is not predicted by the evolutionary biology of congeneric species because sympatry of even morphogically and ecologically quite divergent pupfishes has usually resulted in hybridization/introgression. Survey of variation at eight microsatellite loci reveals that sympatric normal and bulldog populations are genetically distinctive by several criteria, and are therefore likely reproductively isolated. The bulldog morph in Crescent Pond is markedly divergent from those in Little Lake and Osprey Lake, a finding consistent with, although it does not prove, separate parallel origins of this morphotype. The data also suggest that the bulldogs in the latter two lakes did not evolve by intralacustrine speciation from the current sympatric normal populations. Some of the genetic data suggest that the bozo morph may also be reproductively isolated from the other two pupfishes, but only a small, pooled sample of this rare morphotype was available, and the issue is not resolved. Isolating mechanisms between bulldog and normal morphs are of special interest because of the possibility that they arose as a consequence of a predator–prey relationship. A strong correlation between reproductive isolation and predator–prey interactions could provide an important example of ecological speciation via direct selection against heterotypic interactions. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95, 566–582.