We investigated distribution and sexual composition of founding associations of Reticulitermes kanmonensis, the Japanese subterranean termite, which occurs only in the Kanmon area. These properties are discussed in relation to body size and mitochondrial genotype of the dealates. The founding colonies showed a highly aggregated distribution with a ‘hot spot’ of colony founding; however, mitochondrial haplotypes of the dealates suggested random mating. Monogamous colonies were predominant, but solitary colonies and colonies with two females and/or males also occurred. Paired dealates tended to be larger than solitary founders, suggesting that both sexes were under sexual selection related to body size.