The breeding structure of both colony and population of social insects can be examined by genetic analysis. Colonies of the leaf-cutting ants Acromyrmex heyeri and A. striatus (Myrmicinae, Attini) were thus analyzed for isoenzyme systems MDH, a-GPDH, and AMY to describe genotype variability and social structure. A total of five loci were investigated (three for amylase and one for each other system). Ninety-seven colonies of A. heyeri and 103 of A. striatus were sampled in different localities in Southern Brazil (State of Rio Grande do Sul). The genotypes found show the occurrence of monogyny and polygyny associated or not with polyandry, which indicates that the social organization is colony-specific. The polygyny and polyandry observed are likely to be responsible for the great genotypic diversity of the colonies. The average inbreeding coefficient per colony was higher in A. striatus than in A. heyeri, which may reflect the different patterns of production of sexual individuals and nuptial flight of those two species.