[Objectives] To determine the mitochondrial gene sequence of Sinomicrurus peinani, a new species of cobra family, and explore its phylogenetic relationship with related species. [Methods] We used the online software Feature Extract 1.2L server (http://www.cbs.dtu.dk/services/FeatureExtract). The protein coding regions of mitochondrial genome of S. peinani were extracted, and the proportions of four bases and base deviation of different genes were calculated by bioedit (Donath 2012). The online software tRNAscan-SE 2.0 was used (http://lowelab.ucsc.edu/Trnascan SE) to predict the type and secondary structure of tRNA according to antisense codon and isotype model (Lowe et al. 1997), Conventional methods were used to analyze the base composition of triplet codon position, codon usage, the influence of base composition on codon preference and parity preference, and MEGA7.0 was used to construct phylogenetic tree. [Results] The results showed that the mitochondrial genome of S. peinani was a 19477 bp circular DNA molecule, and the genomic bases were A (33.4%), T (28.1%), C (26.6%) and G (11.9%), which encode 38 genes including 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein coding genes and 1 replication origin gene (D-loop). The 13 protein coding genes use AUG as the starting codon and UAA and UGA as the termination codon. The amino acids with high coding frequency of protein coding genes were Leu, Ile, Thr and Ser, respectively; The four codons with the highest frequency of Relative synonymous condon usage (RSCU) were CGA, UGA, CUA and CCA. All 22 tRNAs except tRNASer (with one arm and two rings) could form typical clover structure. [Conclusion] Phylogenetic analysis showed that S. macclellandi was most closely related to the taxonomic status of S. peinani, followed by Naja kaouthia and Ophiophagus hannah (Fig. 2, 3, 6).