In this present study we randomly collected 15 samples of Sinularia from Sanya coral reefs which there are belonging to 7 species including Sinularia grandilobata (1 specimen), Sinularia flexibilis (4 specimens), Sinularia querciformis (1 specimen), Sinularia humilis (2 specimens), Sinularia ceramensis (2 specimens), Sinularia humesi (2 specimens), and Sinularia slieringsi (3 specimens). Both COI and 28S markers used to study inter-specific genetic variation in Sinularia. Based on this, the specific genetic variation analysis within the genus was analyzed. The results showed that the 28S sequence of Sinularia is higher than the mitochondrial COI sequence.