Colonies of the termite Nasutitermes corniger often contain multiple reproductive queens and kings. We used double–strand conformation polymorphism (DSCP) analysis of mitochondrial DNA (mtDNA) to determine the probable origins of co–occurring reproductives. Colonies differed in queen and king number, in the number of nests containing reproductives, and in the genetic relationships among reproductives. Most of the 44 colonies contained a single pair of maternally unrelated reproductives. In the two single–nest colonies with a pair of queens, the two queens differed in mtDNA haplotype, suggesting nest–founding by unrelated queens. In the seven single–nest colonies with larger numbers of reproductives (11–49), all reproductives shared the same haplotype, a pattern consistent with replacement of a single pair by several offspring. As predicted by theory, the number of coexisting queens was greater for replacement reproductives than for co–foundresses. Several complex colonies contained multiple queens of two or more haplotypes distributed among several interconnected nests. This indicates that several matrilines can persist within a colony through one or more generations of budding and replacement, a hypothesis confirmed by orphaning experiments. The various modes of termite colony formation rival the diversity seen in ant species and demonstrate the remarkable convergence of behaviours between the two groups.