The use of natural lacquer for preservation and decoration of various commodities is a remarkable invention. In Japan lacquer production dates back to the Neolithic Jomon period and has been mainly based on the sap extracted from the lacquer tree (Toxicodendron vernicifluum (Stokes) F.A. Barkley). However, it is still unclear, if lacquer production evolved in Japan independently or was introduced from Neolithic China, another centre of early lacquer production. A debate also revolves around the origin of the lacquer tree itself and whether it occurs in Japan naturally or was introduced from the continent along with the skills required for lacquer production. Records of Rhus/Toxicodendron fruit remains, recovered from cultural layers of archaeological sites and natural palaeoenvironmental archives across Japan, provide an opportunity to answer the existing questions. This paper presents a method for differentiating charred endocarps of the six Rhus/Toxicodendron species growing in Japan, which is not feasible based on size or morphological properties of whole fruits or endocarps. To develop this method, we used a set of modern reference fruits. Identification is based on the species-specific tissue structure of the charred endocarp in longitudinal sectional view observed by scanning electron microscopy (SEM). We suggest a simple identification key that is based on two prominent traits of the endocarp’s tissue structure, i.e., tissue alignment and density. The method was successfully applied to an abundant record of charred Rhus/ Toxicodendron endocarps recovered by flotation from Okhotsk culture layers dating to ca. 490–880 CE at the multi-component Hamanaka 2 archaeological site, Rebun Island, Hokkaido region, northern Japan. The recovered endocarps belong to Asian poison ivy (Toxicodendron orientale Greene, 1905) and the chronology of the archaeobotanical assemblages suggests that fruits and/or other parts of this plant were used by different local populations over a period of up to 3000 years (Final Jomon to Classic Ainu period). This indicates that not only lacquer tree was an important economic plant in Japanese prehistory, but also other Rhus/Toxicodendron species were used for unknown purpose. While use of T. orientale for medical effects or as an alternative source for lacquer production seems possible, we hypothesise that at Hamanaka 2 it was utilised for its high tannin content to tan hides and furs of sea mammals. This interpretation emphasises the discussed function of Hamanaka 2, famous for its rich zooarchaeological record of sea mammal remains, as an important site of marine hunting and raw material processing.