The structure and related substitution rate of mitochondrial DNA displacement loop ( D-loop) region and cytochrome b ( Cyt b) were comparatively analyzed through Bayesian MCMC simulation in present study. Based on the sequence analysis of mtDNA D-Loop 648-680 bp,the D-Loop structure of this species is similar to that of other fish species containing the extended termination associated sequence domain ( ETAS),the central conserved domain ( CD) and several conserved sequence block ( CSB-F、CSB-E、CSB-D、CSB-1 ) .According to comparative analysis of related substitution rate in Neosalanx taihuensis,the rate of polymorphic loci was lower in D-Loop (0. 83% ) than in Cyt b (1. 31% ) and the interval estimation of related substitution rate is 1. 000 ± 0. 131 in Cyt b and 0. 859 ± 0. 261 in D-Loop,respectively,which indicated that the mutation rates of D-loop were slower than that of Cyt b with large variance of Bayes posterior density distribution in N. taihuensis. It provided evidence that the substitution rate of Cyt b is higher than that of D-Loop,and is more approximate to molecular clock hypothesis,which indicated that Cyt b might be more appropriate molecular marker than D-Loop in studies on molecular ecology and phylogeography for this species.