Understanding genetic structure and connectivity between populations of freshwater mussels is essential to effective conservation.  We examined two congeneric species of freshwater mussels, Quadrula pustulosa (QP) and Q. quadrula (QQ) throughout their ranges, including the Upper Mississippi, Lower Mississippi, Ohio, Hudson Bay,  and Great Lakes watersheds.  Use of congeners reduces taxonomic distinctiveness, allowing comparisons of differences in life history.  We sequenced approximately 550 base pairs from the mitochondrial COI gene for 263 QP and 147 QQ individuals.  While QP had more unique haplotypes than QQ (0.44 unique haplotypes per individual versus 0.30), sequences from QP were more closely related to one another than those of QQ (5.06 versus 9.74 nucleotide differences within population).  An AMOVA attributed more genetic structure to the population level in QP than QQ (>90% compared to 47%).  Both species had significant structure within populations, among populations, and among regions.  QP exhibited isolation-by-distance, while QQ inter-population genetic distances did not increase with geographic distance.  Both species exhibited reduced diversity with increased latitude, likely the result of recolonization after glaciation.  Other differences between these species may be attributable to host use, evolutionary history and other life history traits.