Molecular genetic techniques have made contributions to studies on subterranean termites at all levels of biological organization. Most of this work has focused on Reticulitermes and Coptotermes, two ecologically and economically important genera. DNA sequence data have significantly improved our understanding of the systematics and taxonomy of these genera. Techniques of molecular biology have provided important new insights into the process of caste differentiation. Population genetic markers, primarily microsatellites, have furthered our understanding of the life history, population biology, community ecology, and invasion biology of subterranean termites. Recent results on the behavioral ecology of subterranean termites reveal a picture different from long-held views, especially those concerning colony breeding structures and foraging ranges. As additional molecular tools and genomic resources become available, and as more subterranean termite researchers incorporate molecular techniques into their approaches, we can expect accelerating advances in all aspects of the biology of this group.