Species identification of 1, 048 eel individuals, collected in the natural waters of middle and western Japan from August 1997 to February 1998, has been performed by polymerase chain reaction (PCR) of the mitochondrial DNA (mtDNA) cytochrome b region. The majority of the individuals (832, 79.4%) were identified as Japanese eel Anguilla japonica. The other individuals (216, 20.6%) were thought to be European eel A. anguilla based on the analysis of PCR restriction fragment length polymorphism (PCR-RFLP). The European eels were found in the samples from Shinjiko Lake (161 out of 513, 31.4%) and Mikawa Bay (55 out of 443, 12.4%). European eel is not a native species in Japan. The possible reasons for the existence of this species in the natural waters of Japan and its influence on the natural resource of Japanese eel are discussed.