The Japenese eel Anguilla japonica is generally assumed to be composed of a single population with wide distribution range, and some genetic studies using allozyme or mitochondrial DNA methods supported this population model. However, one genetic study suggested the existence of multiple populations in this species, and thus, more detailed studies on the population structure of this species is needed. Here, we characterized a total of twenty-one microsatellite markers of the Japanese eel. These will serve as powerful tools for detailed population study for the Japanese eel, though some of them showed the significant departure from the Hardy-Weinberg expectations.