Wolbachia is a common group of intracellular bacteria found in arthropods and filarial nematodes. Since the past decade they have attracted considerable interest owing to their various effects on hosts, which range from reproductive manipulation to mutualism. Moreover, they can influence the mitochondrial DNA pattern which do not reflect the real evolutionary history of the target species and may be incongruent with nuclear data.Previously Wolbachia-manipulated mtDNA patterns, namely mito-nuclear discordance and deep mitochondrial splits associated with specific Wolbachia infections have been also discovered in the genus Maculinea. Here we present a comprehensive study on Wolbachia infestation and the genetic diversity of all Maculinea species in the Carpathian Basin. The prevalence and the pattern of the infestation highly differ among Maculinea species. M. alcon and M. arion are infected in 100%, each of these species with a single strain, but the infection level of M. nausithous and M. teleius is much lower, additionally, they are infected with multiple strains. The genetic diversity of Maculinea species proved to be generally low, only M. nausithous showed geographic pattern based on mitochondrial sequences and allozymes. In contrast with the previous studies, we could not detect mitonuclear discordance or find evidence for Wolbachia-induced selective sweep. Based on our results, we cannot hold only Wolbachia responsible for the restricted genetic diversity of Maculinea in the Carpathian Basin.Probably several factors shape together the level and pattern of genetic variability in Maculinea butterflies.