We analyzed the parentage of Chinese white-bellied rats (Niviventer confucianus) that were mark-recaptured from July 2009 to November 2010 on two islands in Thousand Island Lake, Zhejiang Province, by using eight highly polymorphic microsatellite loci, and explored the characteristics of the relatedness between family groups. These eight loci can indicate the parentage of Chinese white-bellied rat populations on the two islands reliably. According to the results, 71 individuals from island A were divided into 12 family groups, the largest of which contained 19 members. The 49 individuals from island B were divided into 11 family groups, the largest of which contained 14 members. The relatedness of male-female pairs for reproduction (M-F pair) was lowest compared with other pairwise comparison, suggesting that the Chinese white-bellied rats could avoid inbreeding. Relatedness of male-male (M-M) and female-female (F-F) among offspring showed inconsistent performances between island A and island B, suggesting different dispersal particularities. Relatedness of the individual pairwise mating with the same male or female provided some information regarding mate choices. We considered that Chinese white-bellied rats preferred to choose the mates with low relatedness.