Longgu ("dragon bone," Ryu-kotsu, Fossilia Ossis Mastodi, or Os Draconis) is the only fossil crude drug listed in the Japanese Pharmacopoeia. All longgu in the current Japanese market is imported from China, where its resources are being depleted. Therefore, effective countermeasures are urgently needed to prevent resource depletion. One possible solution is the development of a substitute made from bones of contemporary animals that are closely related to the original animal source of the current longgu. However, no research has been conducted on the original animal source of longgu, except for a report on the longgu specimens present in the Shosoin Repository. Taxonomic examination was performed on the fossil specimens related to longgu which are owned by the Museum of Osaka University, Japan. In total, 20,939 fossil fragments were examined, of which 20,886 were mammalian fossils, and 246 of these fossils were classified into nine families. The longgu specimens from the Japanese market belonged to a relatively smaller variety of taxa than those from the Chinese market. Despite the variety of taxa in longgu, medical doctors using Kampo preparations with longgu have not reported any problems due to the presence of impurities in the original animal source. These results suggest that the effect of longgu is independent of its origin as long as it is closely related to the origin of the current longgu. Thus, despite the considerable effects of fossilization, our results could help in developing an optimal substitute for longgu.