Carassius auratus in the Ryukyu Archipelago includes both indigenous and introduced populations which can be discriminated from each other by mitochondrial DNA (mtDNA) haplotyping. MtDNA haplotyping of 485 fish from38 water systems on 11 islands within the Archipelago, showed them to comprise254 (52%) indigenous and 231 (48%) introduced individuals. Indigenous specimens were widespread throughout the Ryukyus, mainly inhabiting natural water systems. Introduced specimens were encountered sporadically, mainly in artificial water systems, especially in reservoirs. Ploidy examination by flow cytometry showed that indigenous populations comprised only diploid or diploid and triploid fish, whereas introduced populations often comprise only triploids. The fact that C. auratus was not found on some islands surveyed, despite their former presence being confirmed, suggested recent decreases of C. auratus and highlighted the importance of future conservation of indigenous Ryukyuan C. auratus.
