Analysis of mitochondrial (16S) and nuclear (H3) gene data using phylogenetic and population genetic approaches has revealed some genetic differences between two putative species of western Atlantic Dondice opisthobranchs that feed differentially on hydroids or on up-side-down jellies of the genus Cassiopeia. These results partially support the validity of the species Dondice parguerensis, which was described for the jelly-eating Dondice. However, phylogenetic analyses revealed that the hydroid-feeding species Dondice occidentalis and D. parguerensis are not reciprocally monophyletic and they are identical for the nuclear H3 gene. Although there are morphological and developmental differences between these two nominal species, the molecular data are inconclusive. A possible explanation is that the two putative species are in the process of speciation due to different feeding habits, resulting in the presence of genetic synapomorphies in D. parguerensis, but only in the more variable 16S gene. Because the ranges D. occidentalis and D. parguerensis overlap and there are no obvious barriers to gene flow between the two putative species, this may constitute a possible example of incipient sympatric speciation in benthic marine organisms.