We investigate the structure between and within colonies of Schedorhinotermes lamanianus (Isoptera: Rhinotermitidae) at a cluster of foraging galleries in Shimba Hills National Reserve, Kenya. Three independent methods (morphometrics of minor soldiers, multilocus fingerprinting from genomic DNA of workers, and aggression tests between workers) yielded concordant results concerning number and spatial extent of colonies as well as variation between and within colonies. At least three colonies exist in our study area. Genetic data reveal that the largest colony is genetically and spatially substructured in three subsidiary nests, which may form reproductive units. These subsidiary nests were not completely isolated as we were able to document exchange of workers. Subsidiary nests may facilitate foundation of colonies by budding which may generate isolation by distance (population viscosity).