Abstract: Collichthys lucidus and C. niveatus are commercially important fishery resources in China. Partial nucleotide sequences of mitochondrial DNA 16S rRNA and Cyt b gene fragments were sequenced and analyzed to study the relationship between C.lucidus and C. niveatus. Forty-four nucleotide substitutions were detected among 16S rRNA (526 bp) and Cyt b (379 bp) fragments. Nucleotide composition analysis indicated that the content of guanine (G) was relatively low in the two fragments, especially at the third codon position of Cyt b genes. Average genetic distances based on 16S rRNA and Cyt b between C.lucidus and C. niveatus were 0.012 and 0.111, respectively. The phylogenetic tree showed that there was significant genetic divergence between C.lucidus and C. niveatus. According to the evolutionary rate of 2% per one million years, the estimated divergence time between C.lucidus and C. niveatus was 5.5 million years, which indicated an early Pliocene divergence for them.