In order to determine the genetic diversity of Takifugu rubripes at five main culture areas in China, twenty pairs of microsatellite primers were tested on populations from Wendeng (WD), Laizhou (LZ), Japanese 1(J1), Japanese 2 (J2) and Tanghai (THQ). It was found that 12 pairs (60%) of the primers displayed polymorphism. The number of alleles of the five populations ranged from 2 to 8, and the average observed heterozygosity was 0.27, 0.26, 0.18, 0.25, 0.20, respectively; the average expected heterozygosity was 0.55, 0.57, 0.69, 0.71, 0.62, respectively; the order of polymorphism information content (PIC) was J2(0.65)＞J1(0.63)＞THQ(0.55)＞LZ(0.51)＞WD(0.48). The results showed that: (1) genetic distance between WD and LZ was 0.233 6, which was the lowest; the genetic distance between LZ and J1 was 0.624 2, which was the highest; (2) the genetic diversity of WD was moderate (0.25＜PIC＜0.5), while that of LZ, J1, J2 and THQ were relatively high (PIC≥0.5). The analysis showed that the genetic diversity of T. rubripes at China’s main culture regions was very high, and therefore, the populations had relatively high potential for genetic improvement.