When deciding to mate, it is assumed that females choose males bearing genes that will improve the genetic quality of their offspring, which is affected by both additive and nonadditive genetic variation. In this context, a ‘compatible genes’ model has been put forward to explain female mating decisions. According to this model, females are assumed to increase the genetic quality of their offspring by choosing mates on the basis of interactions between maternal and paternal genomes. Yet, this model is mainly supported by empirical data in endotherm vertebrates. Few studies have investigated this issue in terrestrial ectotherms like amphibians. These organisms often live in spatially structured populations characterized by small subpopulations and a high degree of philopatry, leading to striking reduction in gene flow, high genetic drift and relatively high inbreeding levels. In such a situation, one might expect that natural selection should favour mating tactics limiting the risk of inbreeding depression. In this paper, using an experimental approach controlling for the reproductive state of males, we examined how genetic compatibility may affect mating behaviour in an anuran, the yellow-bellied toad, Bombina variegata. First, our analyses confirmed a high degree of inbreeding in the studied population. Yet, we did not find any mating tactic that reduced the risk of inbreeding depression. Contrary to our expectations, males more closely related to the female had the higher mating success. We discuss the ecological and evolutionary implications of these results.