Myrmica scabrinodis is one of the commonest European ant species, but field observations of variable ecology and behaviour have suggested the existence of several ecotypes or even cryptic species within this ant.To address this hypothesis, we reconstructed the molecular phylogeny of M. scabrinodis and 15 related species based on 1089 base pairs of mitochondrial genes cytochrome B (Cyt‐B) and cytochrome oxidase subunit I (COI).We show that two major lineages occur throughout Europe. The observed sequence divergence between the two M. scabrinodis lineages is similar to or greater than that observed between the other investigated species.On a local scale, the lineages are both observed at the wet and dry extremes of the overall M. scabrinodis niche distribution, but analysis of the Myrmica communities in two sympatric populations shows that lineage B tends to avoid the drier habitat patches.Our inferred phylogenetic relationship of intra‐ and inter‐specific mitochondrial lineages within the M. scabrinodis species group in general shows several inconsistencies with the presently accepted taxonomy, suggesting the potential existence of more unrecognised cryptic species.The separate status of other species is not supported, particularly the differentiation between Myrmica sabuleti and Myrmica lonae, and specimens identified as Myrmica tulinae have highly inconsistent mitochondrial haplotypes, suggesting that the morphology associated with this taxon does not reflect phylogeny.The existence of multiple lineages within M. scabrinodis, and the apparent synonymy between M. lonae and M. sabuleti has implications for the conservation of Maculinea butterflies, for which these are major hosts.