The genus Elassoma represents a small but unique component of the aquatic biodiversity hotspot in southeastern North America. We present the first phylogeny of the seven described species, corroborated by sequence data from mitochondrial and nuclear protein coding genes. This analysis reveals a Coastal Plain clade sister to the geographically isolated, and federally protected, Elassoma alabamae. The Coastal Plain clade contains the widespread E. zonatum, which is sister to a clade primarily restricted to lowland Neogene subprovinces. We analyzed morphometric data in a phylogenetic context to illustrate the evolution of sexual shape dimorphism within the genus. Sixteen univariate and three multivariate traits were tested for significant sexual dimorphism for each species, and relative transformation rates were inferred from the time tree. A simple index of interspecific sexual dimorphism revealed greater disparity among sympatric species comparisons than among allopatric comparisons. Results implicate geology as a primary factor influencing ecological diversification, and sexual selection as a mechanism reinforcing reproductive isolation in areas of secondary contact. We discuss putative roles of geological history and sexual selection in the generation and maintenance of the aquatic biodiversity gradient in southeastern North America.