Freshwater bivalves in the family Unionidae are one of the most endangered groups of animals in North America. In Texas, where over 60% of unionids are rare or very rare, 15 species have been added to the state's list of threatened species, and 10 are under consideration for federal listing. Due to insufficient survey efforts in the past decades, however, primary data on current distribution and habitat requirement for most of these rare species are lacking, thus challenging their protection and management. Although the species are listed as valid, there was no genetic confirmation to test for the possibility of ecophenotypes, which complicates conservation efforts. In this paper, we present genetic and distributional data for two rare Texas species, Truncilla macrodon and Truncilla cognata, and we suggest appropriate conservation measures. Tests of genetic affinities of these species using three gene regions, cox1, nad1 and ITS1, supported recognition of T. cognata and T. macrodon as full species. Analysis of historic and current species distribution showed that both these regional endemics are particularly vulnerable, and their distribution range has been reduced in the last 80 years.