Abstract: Using RAPD and ISSR molecular marker technology,genetic diversity of 80 samples of 8 natural populations of Bemisia tabaci collected from 7 regions of Fujian province, China was studied in this paper. The 2240 and 1776 bands were amplified respectively with 4 RAPD primers and 4 ISSR primers from the DNA of 80 samples, and among them, 2000 and 1728 bands were polymorphic respectively. The results showed that genetic diversity of B. tabaci in natural populations were quite abundant in Fujian. According to the UPGMA clustering based on the genetic distance between the populations, the 8 populations were classified into 2 groups. One group was only Longhai population(host:Codiaeum variegatum), which could be illustrated that it kept at a distance with other populations on genetic relationship. We inferred that it was possible a different biotype with others. In addition, a certain correlation was observed between the geographic distance and the genetic distance of the populations.