The most recent evaluation of Fundulus nottii, the Bayou Topminnow, reports that it occurs in several river drainages in the panhandle of Florida. However, recent reidentification of the morphology of those specimens, with only one exception, suggests that these represent the similar Russetfin Topminnow, Fundulus escambiae, which is common throughout the panhandle. Though the two species are typically distinguished by color pattern, they are otherwise morphologically similar which makes them difficult to separate through typical morphometric measurements. Because Fundulus notti and Fundulus escambiae are currently recognized as sister species, the objective of this study was to determine whether Fundulus escambiae is a genealogically distinct lineage from Fundulus nottii. Assuming Fundulus notti and Fundulus escambiae are valid species we sampled species across their known range and hypothesized that the genetic data would support two reciprocally monophyletic groups that are in line with the current taxonomy. To test our hypothesis, we utilized phylogenetic analysis of DNA sequence data, created a haplotype network and completed analysis of morphological characteristics. Our data showed that the species hypothesis of Fundulus notti and Fundulus escambiae was not supported by either the morphological or genetic data. Thus, we reject our hypothesis and refute that these are not two reciprocally monophyletic groups. Fundulus escambiae is a monophyletic group nested within the genetic diversity of Fundulus nottii.