As major river drainages separated and stream capture occurred, some populations of Xiphophorus fishes became geographically isolated from one another, while others came into contact with new Xiphophorus species. Sexual communication and mechanisms of reproductive isolation were likely influenced by the variation in community structure each population experienced. One swordtail species, Xiphophorus birchmanni, occurs both in streams where other Xiphophorus species are rare, or more typically with large populations of congeners. Using the X. birchmanni system, we tested the theory that species recognition should be favored when the opportunity for hybridization is high. We found that at a site where the congener, X. variatus, is the predominant species, female X. birchmanni have a strong preference for conspecific cues; however, female X. birchmanni from a location where X. variatus are rare do not discriminate between conspecific and heterospecific cues. Moreover, we show evidence that chemosignals used by male X. birchmanni to attract females are unique between the two populations that differ in community structure. Our findings suggest that not only can the presence or absence of a congener influence sexual communication, both in terms of female preference and male trait, but the abundance of congeners may also be an equally important source of interpopulation variation.