Until recently, morphology has been the predominant basis on which taxonomic decisions have been made. Now, many sources of data inform decisions in taxonomy, yet few studies are available that directly compare the conclusions made on the basis of different datasets. The difficulty of reaching clear taxonomic decisions is further complicated by the existence of allopatric populations, which may differ from other populations in notable ways yet not be distinct evolutionary units. We analyzed differences at the molecular level based on sequences of two mitochondrial genes, analyzed acoustic differences in male vocalizations (nine variables) and conducted a phonotaxis experiment with females to assess the taxonomic status of two putative Caribbean frog species (Mannophryne olmonae and Mannophryne trinitatis, Aromobatidae), which some authors have indicated as conspecific. A 16S gene tree (75 sequences of 15 putative species, 530 bp), a parametric bootstrap test, and the results of acoustic comparisons suggested that these entities were evolutionarily distinct. However, in the phonotaxis experiment, females of either species did not display significant preference among the male vocalizations presented. On the basis of the bioacoustic data and the 16S gene tree, we conclude that these taxa are distinct and suggest that lack of selection for pre-mating isolation in allopatry explains the lack of discrimination shown by females. Phonotaxis experiments in taxa with acoustic means of mate attraction should continue to be useful in assessing the evolutionary independence of putative sympatric entities, but our results suggest that they should be employed and interpreted cautiously when applied to allopatric populations. To most accurately assess the boundaries of evolutionary lineages, a pluralistic approach, utilizing as many sources of data as possible, is desirable.