Cyprinidae fish are widely distributed in Taiwan, and processed products made from them are favored by consumers. To identify the species used for these processed products, complete mitochondrial cytochrome b genes (cytb, 1141 bp) of 8 Cyprinidae were established. Then, a rapid PCR–RFLP method was used to amplify a 426 bp fragment of cytb using primer set Lnew1/Hnew1, and the fragment was co-digested with NlaIII and BstXI. The results show that using this PCR–RFLP technique for the species identification of the 8 Cyprinidae was successful. The method was further applied to investigate 16 commercial samples of processed Cyprinidae products from traditional markets. The results indicate that 9 of the samples were Carassius auratus auratus, Cyprinus carpio carpio, or Ctenopharyngodon idella. The other 6 samples did not belong to the Cyprinidae family according to PCR–RFLP. These samples were further analyzed with the forensically informative nucleotide sequencing (FINS) and BLAST methods. The results show that these 6 processed products were Oreochromis spp., a monophyletic fish group. The last commercial product could not be amplified to obtain a 426 bp fragment, so its species remains unknown. This study shows that PCR–RFLP and FINS can be used to identify processed products fraudulently labeled as Cyprinidae.