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The bacterium  Wolbachia  infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of  Wolbachia  infection and mitochondrial diversity in two systems:  Aricia agestis / Aricia artaxerxes  and the  Pseudophilotes baton  species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two  Wolbachia  genes. Both butterfly systems had uninfected and infected populations, and harboured several  Wolbachia  strains.  Wolbachia  was highly prevalent in  A. artaxerxes  and the host’s mitochondrial structure was shallow, in contrast to  A. agestis . Similar bacterial alleles infected both  Aricia  species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the  P. baton  species complex mirrored its  Wolbachia  infection and not the taxonomical division.  Pseudophilotes baton  and  P. vicrama  formed a hybrid zone in Europe.  Wolbachia  could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for  Wolbachia  should be routine in mitochondrial DNA studies.

Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies