It is commonly held that Central Europe harbours but a single harvester ant species, namely Messor structor. Recently discovered bionomic differences between two Central European populations, which may reflect interspecific variation, cast doubt on this assumption. In the present study we test alternative hypotheses - one versus two harvester ant species in Central Europe and adjacent regions - by investigating the genetic diversity of ants determined as M. structor or close to it ("M. cf. structor"). Sequences of the mitochondrial COI gene revealed two major lineages of different but partially overlapping geographic distributions, both occurring in Central Europe. The existence of a cryptic species within M. cf. structor is the most plausible interpretation, since the sequence divergence between the two major lineages equals those between M. capitatus, M. concolor and M. bouvieri. The phylogenetic analyses revealed a distinct substructuring for both of the detected major lineages and the possible existence of additional cryptic species.