We analyzed 88 control region sequences of green sea turtle (Chelonia mydas) from around Hainan Island in the South China Sea. These sequences had a length of 489 bp and revealed 8 mtDNA haplotypes of which four haplotypes (CMC1, CMC4, CMC7, and CMC8) had not been discovered before. Haplotype diversity (h) and nucleotide diversity (π) were 0.45 ± 0.054 and 0.0035 ± 0.0014, respectively. Neighbor-Joining tree based on control region sequences revealed that genetic relationship between green sea turtles from the South China Sea and from Japan Sea were very close. Clustering relationship based on control region sequences indicated that the South China Sea is an important breeding site and feeding habitat for green sea turtles, which connects with the Middle East Pacific, the Southwest Pacific and the Indian Ocean.