Nansha Islands and Xisha Islands comprise the two largest coral reef archipelagoes in the South China Sea. Biota study on the Xisha Islands started from the 1950’s. Many papers about the fauna and flora there have been published. Biological expeditions to the Nansha Islands started later, and biota study there, compared to that in the Xishas, is also less. The present paper compares with the benthos between the two archipelagoes. The reported families, genera and species number are 309, 663+, 1570 in the Xisha Islands and 309+, 837, 1444 in Nansha Islands. Although benthos study on the Nansha Islands is less than that on the Xisha Islands, the rich species in the Nanshas indicates that the biodiversity there is higher than that in the Xisha Islands. Because stronger and stronger human activities, and global warming, the coral death in the Nansha Islands is much more than before, and the organisms living in coral reefs are also less and less. Research on the biodiversity and protection of coral reefs in the Nansha Islands should be strengthened.