Forward inner primers, backward inner primers and forward and backward outer primers were designed for discriminating between the single nucleotide polymorphisms of exons 10 on the genomic DNA that encodes endo-beta-1,4-glucanase of two subterranean termites, Reticulitermes speratus and Coptotermes formosanus. Using these primers, the loop-mediated isothermal amplification (LAMP) method successfully amplified genomic DNA that was extracted from the heads of R. speratus and C. formosanus, but failed in amplifying genomic DNA of R. speratus and C. formosanus that was extracted from galleries constructed by the termites.