Lethrinus olivaceus is an important coral reef fish in the South China Sea. To reveal the genetic structure and genetic diversity of L. olivaceus, a 495 bp segment of mitochondrial DNA control region was sequenced. We collected a total of 65 individuals from three archipelagos (Xisha, Zhongsha and Nansha) in the South China Sea and 107 polymorphic sites were obtained defining 39 haplotypes. Based on the NJ tree, two distinct lineages were detected, with strong frequency differences in the geographical distribution. Both lineages were found in Xisha and Zhongsha archipelagos, but only one lineage (lineage B) was detected in Nansha archipelago. Contrary to homogenization expectation, AMOVA and pairwise FST values showed that the genetic differences among three archipelagos were all significant. The pattern of population demography showed sudden expansion model in lineage A and stable model in lineage B. These results indicated that there might be three different fishery management units of L. olivaceus in the South China Sea. Each of archipelagos should be treated as one independent management unit.