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The comple mitogenome of Spanish flag snapper, Lutjanus carponotatus was determined by next generation sequencing (NGS) technique. The mitogenome of L. carponotatus (16,514 bp) habors 37 genes (22 tRNAs, 2 rRNAs, 13 polypeptides) and two non-coding regions, the origin of light strand replication (OL) and the putative control region (D-Loop). Among the 37 genes in L. carponotatus mitogenome, 28 were encoded on the H-strand, whereas only 9 were on the L-strand. Phylogenetic relationship showed that the full mitochondrial genome sequences L. carponotatus was most closely related to Lutjanus russellii with 93% sequence identity clustering with Lutjanus fulviflamma (92%) and Lutjanus vitta (91%).