Attempts were made to establish specific polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) profiles of 10 different Cyprinidae fish species using capillary electrophoresis (CE). The primer set CypbL/CypbH was used to amplify a partial mitochondrial cytochrome b gene (331 bp), and the product was subsequently co-digested with endonuclease (NlaIII and MseI). The PCR-RFLP profiles of the 10 Cyprinidae fish species determined using CE were able to successfully differentiate the different fish species. This method was further applied to detect the species used in 24 commercial Cyprinidae-related products. The results identified 4 samples as Cyprinus carpio carpio, 8 samples as Carassius auratus auratus, and 12 samples as Ctenopharyngodon idella. This study shows that performing PCR-RFLP in a CE system is useful for identifying the species of fish from which the processed products originated, and this method can be a potential analytical tool for large and routine food authentication in the future.