In this study, the three species morphometric character was analysed and its certain character were overlapped. So this leads to the further study of protein band pattern for the identification and confirmation. The SDS PAGE protein patterns were used to assess the levels of genetic diversity in Puntius filamentosus, Puntius tambraparanei and Puntius bimaculatus. The number of protein bands and Molecular weight of the band were the difference among the three species. This shows three species are overlapped in certain morphometric character also. Further more this problem may be solved by the mitochondrial DNA markers only.