The symbiotic relationship of termites and their eukaryotic and prokaryotic gut microbiota is a focal point of research because of the important roles symbionts play in termite nutrition. The use of molecular methods has recently provided valuable insights into the species diversity and the roles of microorganisms in the guts of termites. This paper provides a review of the current knowledge of symbiont species inventories, genome analysis, and gene expression in the guts of subterranean termites. Particular emphasis is given to the termite genera Reticulitermes and Coptotermes (Isoptera: Rhinotermitidae), because they contain pest species of global impact in their native and invasive range.