The resinous portions of Aquilaria plants, called agarwood, have been used as medicines and incenses. Agarwood contains a great variety of sesquiterpenes, and a study using cultured cells of Aquilaria crassna showed that the production of sesquiterpenes (alpha-guaiene, alpha-humulene, and delta-guaiene) was induced by treatment with methyl jasmonate, which led to the cloning of delta-guaiene synthases. In the present study, analyses of genomic organization and Southern blotting of delta-guaiene synthase in A. crassna were performed in order to examine the genomic background of delta-guaiene synthases in Aquilaria plants. Genomic cloning and sequencing revealed five types of sequence in putative delta-guaiene synthases sharing more than 96% identity in exon regions, and that these enzymes belonged to the class III TPS subfamily with seven exons and six introns. Furthermore, Southern blotting revealed that at least five copies of delta-guaiene synthase existed in A. crassna. The hybridization of digested DNA of A. crassna and A. sinensis with probes made with a delta-guaiene synthase cDNA fragment resulted in different banding patterns for these two species. It may be possible to identify Aquilaria species by restriction fragment length polymorphism analyses with delta-guaiene synthase cDNA probes.