We used the mitochondrial cytochrome-b gene and four microsatellite-DNA loci to assess levels of genetic introgression between two hybridizing poeciliid fishes in Texas, a locally endemic, endangered species, Gambusia heterochir, and a wide-ranging congener, G. affinis. Past morphological studies indicated a long history of hybridization and backcrossing. We detected ongoing, low-level hybridization, but no evidence of a long-term, evolutionary history of genetic introgression. Only one of 118 G. heterochir (0.9%) might have had an ancestor in G. affinis, but this was weakly supported. We detected one potential F1 hybrid, but it was more likely a recent product of backcrossing between a hybrid and G. affinis. Two other fish were more distant products of such backcrossing. At present, there appears to be little cause for concern regarding the genetic integrity of G. heterochir. The widespread species, G. affinis, showed significant genetic structure over short geographic distances, including divergence between populations on two sides of a small dam with through-flowing water.