Anguillid eels are a high value species for aquaculture in East Asian countries, but natural stocks of eels have been decreasing. Mass production of glass eels is one of the most effective ways to solve this problem. Genetic improvements will become important to establish mass production of glass eels in the near future. However, there is a lack of basic information, such as parentage assignments, for implementing an eel breeding program. In this study, we aimed to understand the parentage assignment of Japanese eel (Anguilla japonica) using a multiple breeding method and microsatellites from eight loci. Five female and 15 male eels were used for mass spawning, and the progeny were collected at the pre-leptocephalus (2 days post-hatch [dph]) and the leptocephalus stage (30 dph). Almost all progeny (297/301 = 98.7%) were assigned to a parental couple. Only two female eels (F86 and F88) contributed to the next generation, whereas 13 of 15 males contributed to the next generation. Although there were no statistical differences in the paternity ratio between stages, some males changed the ratio in both females. These data are not directly useful for a breeding program, but are useful to maintain pedigree information, which is essential for implementing a breeding program.