To identify subterranean termite species, we designed a pair of common primers that amplified 381-bp fragments from cDNAs encoding the endo-β-1,4-glucanases (EGases) of Coptotermes formosanus Shiraki and Reticulitermes speratus (Kolbe). cDNAs from C. formosanus and R. speratus, and genomic DNA from R. speratus, were amplified by polymerase chain reaction (PCR) by using this primer pair and then cloned and sequenced. Sequences amplified from C. formosanus cDNA displayed 97–99% identity to cDNA encoding the EGase of C. formosanus (CfEG), and 92–94% identity to cDNA encoding the EGase of R. speratus (RsEG). By contrast, cDNA from R. speratus displayed 99–100% identity to RsEG cDNA and 93–94% identity to CfEG cDNA. CfEG and RsEG cDNAs can therefore be used as markers for the identification of these termite species. This is the first report of the successful identification of termite species by using cDNA and genomic DNA sequences of termite origin.