Most interactions between individuals of social insect, occur in colonies. The correct identification or colonies is therefore crucial for most empirical studies which aim to rest evolutionary theories based on properties at the colony level. In many ant populations, the identification of colonies is hampered by polydomy i.e. that single colonies occupy several. spatially separated nests. Only few attempts have been made so fir to develop genetical methods for analysing the structure or specific colonies. Three methods to solve this problem are presented: rare genotype sisterhoods (tracking rare genotypes or alleles). G-distance (a measure of genotypic heterogeneity derived from G-statistics). and neighbour relatedness (estimates of genetic relatedness for specific nest pairs). Out methods genetical the likelihood of nest pairs being con-colonial or non-colonial, and Rn en sufficient genetical resolution: statistical levels can be applied. The methods proposed here are applied to a highly polygynous population of the red ant. Myrmica sulcinodis. In this population single colonies are found to inhabit 1-4 nests, rind both monodomous and polydomous colonies coexist in dense clusters of nests. This result is discussed with respect to the functional significance of polydomy. Further, the general application of the methods for determination of colony structure is discussed. (C) 1999 The Linnean Society of London.