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The Florida bog frog (
Rana okaloosae
) is restricted to approximately 25 seepage drainages on the Florida Panhandle, southeastern USA. We evaluated fine-scale (<1–10 km) genetic structure among 80 samples from a long-term study area in one portion of its range. We also included co-distributed samples (
N
= 48) from bronze frogs (
R. clamitans
). Individual
R. okaloosae
were significantly more related to one another than expected under panmixia, though significant patterns of isolation-by-distance were detected reflecting limited dispersal. Bayesian clustering failed to identify discrete genetic clusters within species. Subtle, though important differences in genetic structuring between
R. okaloosae
and
R. clamitans
suggests that future efforts to predict the impact of landscape changes on
Rana okaloosae
, should focus on the species itself rather than
R. clamitans
as a surrogate species.