The population structure of pond-breeding amphibians is shaped by their distinct breeding foci, but it is unclear to what extent this is reflected in the fine-scale distribution of genetic diversity. We used microsatellite genotypes to investigate the genetic signatures of 24 populations of European newts, Triturus cristatus and T. marmoratus, inhabiting 21 ponds in a confined study area (7.5 · 3.5 km) in western France. Employing a Bayesian clustering approach based on individual genotypes that minimises departures from Hardy–Weinberg equilibrium and linkage disequilibrium, no evidence was found for within-pond substructuring. Subjecting all sampled ponds simultaneously to this procedure revealed a clear signal of partitioning, with the most likely number of clusters however below the actual number of ponds (seven in T. cristatus, three in T. marmoratus). A more hierarchical Bayesian approach, with pond as analysis unit, was achieved to separate ponds from genetically more meaningful units, and reduced the T. cristatus populations to 11 clusters, and the T. marmoratus populations to five clusters. We were unable to specify a minimum nearest-neighbour distance where ponds are separate units, probably due to both historical and current demographic processes. The implications for strategies to manage and conserve endangered amphibians in human-altered landscapes are discussed.