The Norway Rat (Rattus norvegicus) is one of the main pest rodents in Hainan Island, where there is an important port in South China. However, its genetic diversity and gene flows between rat populations in Hainan Island and neighbor regions are not clear. In this study, we sequenced the cytochrome b (Cyt b) gene for 91 Norway Rats from Hainan Island, Guangdong Province, Vietnam, Philippine etc., then analyzed the Cyt b haplotypes and the level of population differentiation (Fst), and constructed the phylogenetic relationship among 60 Cyt b haplotypes from the Norway Rats all over the world. Results show that the rat populations from Yacheng and Qiongzhong/Chengmai in Hainan Island share no haplotype (Table 1), furthermore, the two populations are significantly differentiated (Fst = 0.453, Table 2). However, the two Hainan populations shared haplotypes with the rat populations in Guangdong Province and Philippines/Vietnam, respectively (Table 1), indicating possible gene flows between populations in Yacheng and Philippines/Vietname, and between populations in Qiongzhong/Chengmai and Guangdong Province. Phylogenetic analysis reveals that most Cyt b haplotypes in Hainan Island and Guangdong Province cluster into two haplotype groups CⅢ and CⅦ (Fig. 2, 3), indicating that the rat populations in Hainan Island and Guangdong Province may spread from one or more common ancestral populations, which likely spread from coastal region of Guangdong and Guangxi provinces and arrived in Hainan Island with Li people in the middle Neolithic (about 3 000 years ago) or before that time.