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Sonneratia ovata is one of the most widely distributed mangrove species worldwide. In this study, the complete chloroplast (cp) genome of S. ovata was sequenced and assembled; its phylogenetic position was confirmed in Lythraceae. The total size of cp genome was 153,052 bp, exhibiting a typical quadripartite structure with a large single copy (LSC) region of 87,238 bp and a small single copy (SSC) region of 18,002 bp, two inverted repeats (IRs) regions of 23,906 bp each. The overall GC content was 37.3%, respectively. We detected 128 genes in cp genome, including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. A phylogenetic analysis showed that S. ovata has a close relationship with S. apetala within the genus Sonneratia.