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The complete mitogenome of Sardinella zunasi was determined by next-generation sequencing. The S. zunasi mitogenome was a circular 16,307 bp molecule that contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and one control region (D-loop). The gene arrangement was consistent with other Sardinella mitogenomes. The phylogenetic relationships of 29 Clupeoidei species based on 13 protein-coding genes from the available mitogenomes were analyzed. Sardinella zunasi clustered with Sardinella among Clupeidae, suggesting a closer relationship with this genus. These results will be useful for understanding the phylogenetic relationships, taxonomic classification, and phylogeography of the genus Sardinella relative to other genera of Clupeoidei.