Visual implant elastomer (VIE) marking was evaluated as a tool for individual tagging of larval Japanese eels, Anguilla japonica, during rearing conditions. Combinations of eight colors of VIE tag were used to individually mark leptocephalus larvae (104–110 days post hatched) by injecting them with either a mixture of a silicone color material and a curing agent, or only color material. Injections were at three locations on the dorso-lateral body surface for individual identification, and a sham-operated control group was also prepared. Tag retention was 100% with or without curing agent, and individuals could be tracked until larvae completely metamorphosed into glass eels. After some initial mortality, the survival and growth rates were not different between each treatment group. These results suggested that VIE tagging could provide good individual larva identification method for research during rearing conditions.