The complete sequence of mitochondrial genome of Larus brunnicephalus was determined using long PCR and conserved primers walking approaches. The results showed that the entire mitochondrial genome of L. brunnicephalus is 16,769 bp in length, which has been deposited in GenBank with the accession number JX155863. The mitochondrial genomic organization and gene order of L. brunnicephalus were consistent with that of Gallus gallus, which contains 13 protein coding genes (PCGs), 22 tRNA, 2 rRNA, and a control region. Except for COI gene using GTG and ND3 gene with ATT as the initiation codon, all other 11 PCGs of the mtDNA in L. brunnicephalus started with the typical ATG codon. AGG, TAG, TAA, or AGA were used in 11 PCGs as usual termination codons, except for COIII and ND4 genes with incomplete termination codon (T). The secondary structures of 22 tRNAs were predicted and it is found that the tRNASer (AGN) lacks DHU arm and tRNAPhe contains the fourth types of permutation in the TψC arm. It is predicted that the secondary structures of 12S rRNA and 16S rRNA include 4 structural domains with 47 helics and 6 domains with 60 helics, respectively. F-box, E-box, D-box, C-box, B-box, Bird similarity-box, and CSB-boxes (1-3), which were found in the control regions of other bird species were also present in L. brunnicephalus. The sequence in the starting regions of H-strand replication (OH) and the bidirectional light and heavy-strand transcription promoters (LSP/HSP) in the control region were also predicted. Result of phylogeny analysis supports that L. brunnicephalus should be categorized into the Masked gulls species.