The evolutionary stability of social cooperation requires altruistic acts to be directed mainly towards related individuals. To maintain significant intragroup relatedness, social insects have evolved sophisticated recognition systems. We compared nestmate recognition abilities of three native European species of the ant genus Temnothorax in relation to variation in cuticular chemicals and intraspecific genetic diversity. Colony take-over and fusions are common in two sibling species T. nylanderi and T. crassispinus, but rare in T. unifasciatus, suggesting relatively inefficient nestmate recognition in the former species. Temnothorax nylanderi and T. crassispinus discriminated less effectively between nestmates and non-nestmates than T. unifasciatus. While chemical profiles of different colonies strongly overlapped in T. crassispinus and T. nylanderi, 97% of all T. unifasciatus samples were, in a discriminant analysis, correctly assigned to their respective colony. Chemical distances between colonies correlated with aggression levels in T. unifasciatus, but not in the other two species. Finally, preliminary genetic results indicated that haplotype divergence within T. nylanderi and T. crassispinus is remarkably low, whereas T. unifasciatus and other congeners are genetically more variable. In theory, loss of genetic variation, including depletion at loci involved in the production of cuticular hydrocarbons, could decrease colony recognition efficiency. We suggest that this might be the case in T. nylanderi and T. crassispinus, leading to colony fusions in the field. Despite their different life histories, these native species show similarities to invasive ants where genetic bottlenecks arising from founder effects are thought to result in a loss of colony boundaries.