To search for a variety of cellulase genes from termites with different habitats consuming different foods, we collected three species (Neotermes spp., Odontotermes spp., Macrotermes spp.) from the wood and one species (Nasutitermes spp.) from the cow dung. Total RNA was isolated both from alimentary track tissues containing paunch and from other tissues, and used for the suppression subtractive hybridization (SSH). The resulting EST libraries were sequenced and searched by BLAST to identify cellulase genes. A total of 16 cellulase genes were found from the wood-dwelling termites whereas 4 cellulase genes from the cow dung-dwelling termites. Endo-beta-1,4-glucanase and beta-glucosidase were identified as the most abundant cellulase from the wood-dwelling termites and cow dung-dwelling termites, respectively. This finding suggests that cellulase profiles are significantly different depending on the termite’s habitat and food. In addition, we analyzed phylogenetic relationships among the cellulase genes along with other cellulase genes reported to date. All cellulase genes appeared to be originated from endosymbioants without any hint of horizontal gene transfer. Functional expression of endo-beta-1,4-glucanase using a baculovirus expression system is in progress to characterize its enzymatic properties.