Myriad anthropogenic factors have led to substantial declines in North America's freshwater mussel populations over the last century. A greater understanding of mussel dispersal abilities, genetic structure, and effective population sizes is imperative to improve conservation strategies. This study used microsatellites to investigate genetic structure among mussel beds and estimate effective population sizes of a common North American mussel species, Amblema plicata, in the Little River, Oklahoma. We used five microsatellite loci to genotype 270 individuals from nine mussel beds distributed throughout the river and one of its tributaries, the Glover River. Our results indicate that subpopulations of A. plicata in the Little River are genetically similar. Upstream subpopulations had less genetic diversity than sites located downstream of the confluence of the Glover and Little rivers. Downstream subpopulations were primarily assigned to the same genetic group as upstream subpopulations, but they were admixed with a second genetic group. Low flows during droughts likely influenced the observed genetic structuring in A. plicata populations in the Little River. Additionally, downstream subpopulations may be admixed with a genetically distinct population of A. plicata, which may account for the increased genetic diversity. Estimates of effective population sizes (N_e) of large mussel beds were low compared to the total abundance (N) of A. plicata. While our data have limitations, they provide important information on the spatial scale at which conservation plans should focus and the population sizes that should be sustained through relocation and restocking programs.