In the present paper, mtDNA RFLP and mtDNA D-loop sequencing were investigated in three species of Cyprinus from Erhai Lake. The results indicated that two mtDNA haplotypes were identified in three species of Cyprinus from Erhai Lake by using 16 restriction endonucleases. All individuals share the dominant type I except one individual of C. longipectoralis shows type II just with only one cleavage site polymorphism when tested by Dra I. Compared to the reported interspecific and intraspecific sequence divergence in fishes, the present divergence values of 0% - 0.0075% from the Cyprinus species native to Erhai Lake were too much lower. Furthermore, 449 bp of mtDNA D-loop region sequencing was investigated in these three Cyprinus species. There were six mtDNA haplotypes indicated by seven variation sites. The interspecific sequence divergence were 0.082% - 0.171%. It is also at least one degree lower than some allopatric Cyprinus species we studied. A remarkably low level of genetic divergence detected among the three species of Cyprinus species in Erhai Lake both by mtDNA RFLP and D-loop region sequencing provides direct genetic evidence for its sympatric speciation pattern, which could occurred without progressive adaptive genetic variation.