Genetic markers were obtained for the termite Nasutitermes corniger by DSCP (double-strand conformation polymorphism) analysis of PCR-amplified mitochondrial control region DNA. This procedure revealed twenty-one haplotypes in forty-four colonies, whereas a restriction fragment length polymorphism analysis detected only nine haplotypes. Sequence analysis of DSCP fragments of contrasting mobilities suggests that the electrophoretic haplotypes are caused by DNA curvature in this highly AT-rich region. DSCP markers showed that some termite colonies contained maternally unrelated queens, each of which produced worker offspring. This pattern is consistent with nest founding by unrelated queens. Due to the availability of conserved primers for the mtDNA control region, DSCP analysis may readily reveal comparatively high levels of variation in a wide variety of organisms.