We compared the genetic diversities across eight microsatellite loci of two widespread anurans, Bufio bufo and Rana temporaria, at multiple sites across their western and central European ranges. Bufo bufo consistently exhibited less genetic diversity than R. temporaria. Our evidence infers that this difference is unlikely to be a feature of the specific marker loci used, nor is it a probable consequence of the different phylogeographic histories of B. bufo and R. temporaria. No recent bottlenecks were observed in B. bufo or R. temporaria populations. Both species showed similar levels of differentiation across their European range as estimated by F-statistics, but whereas R. temporaria exhibited isolation by distance effects, B. bufo did not. We suggest that distinct autecological features of the two species are the most likely explanation of the diversity differences, especially more limited historical gene flow among Bufio compared with Rana populations.