Agarwood is a type of resinous wood found in the trunks of Aquilaria and some other genera. It is widely used as an herbal medicine for sedation, detoxification, and treatment of stomachaches, as well as for incense sticks. However, the number of source plants is decreasing, and in 2005, they were added to Appendix II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). To identify source species of agarwood, we previously developed a DNA-barcoding method using resin deposition sites. In this study, to identify additional agarwood source species, the barcoding method was applied to source plants and commercial agarwood samples collected from Sumbawa, Lombok, Sulawesi, and Kalimantan in Indonesia, a major agarwood-producing country. In addition, the method was also applied to incense stick samples labeled as agarwood. As a result, several samples were identified as Gyrinops, which is not currently listed as an agarwood source plant in the Japanese standards for non-Pharmacopoeial crude drugs 2018 (Non-JPS 2018). From the viewpoint of securing future resources, these findings suggest that Gyrinops species should, therefore, be added to the list of agarwood source species.