Unionid bivalves have exceptional diversity in southeastern North America, despite high levels of anthropogenic extinction. They are confined to fresh water, so their phylogeny has excellent potential to reflect drainage patterns and the history of connections between drainages. However, the high levels of individual variability and interspecies convergence have greatly limited phylogenetic study. The present study used molecular data for the COI, 16S, and ND1 genes to produce a well-resolved phylogeny and uses it to investigate relationships between the major drainages of the eastern Gulf region. Most drainages have significant endemism, suggesting extended periods of relative isolation with occasional dispersal.