We investigated the genetic population structure of two rare myrmecophilous lycaenid butterflies, Maculinea nausithous and M. teleius, which often live sympatrically and have similar biology. In Europe, both species occur in highly fragmented populations and are vulnerable to local extinction. The proportion of variable allozyme loci, average heterozygosity and genetic differentiation among populations was higher in M. nausithous than in sympatrically living M. teleius populations. We hypothesise that the differences in heterozygosity are mainly due to the known higher efficiency of typical host ant nests in rearing M. nausithous pupae compared to M. teleius pupae. This implies a larger probability of larval survival in M. nausithous, which buffers populations against environmental and demographic stochasticity. In contrast, the lower carrying capacity of ant nests in rearing M. teleius pupae requires higher nest-densities and makes M. teleius populations more prone to losing genetic variation through drift if this condition is not fulfilled. The single investigated Russian population of M. teleius showed much higher levels of heterozygosity than any of the Polish populations, suggesting a more viable and still intact metapopulation structure.