GP5, the most important neutralizing antigen of porcine reproductive and respiratory syndrome virus (PRRSV), has the highest genetic diversity among isolates. To more fully understand the extent of genetic diversity of PRRSV in China, we analyzed and compared the GP5 sequences of 42 PRRSV isolated from 1996 to 2006 in mainland China. We found that all of the Chinese isolates examined belong to the North American (NA) type. Among them two highly diverse subgroups were clearly demarcated on the NA-genotype phylogenetic tree. All the subgroup 1 isolates were found to be high variable in the primary neutralizing epitope and the viruses were geographically restricted to regions in southeast China. The subgroup 2 isolates shared a high identity with MLV vaccine and its parent virus VR-2332. These results may contribute to the knowledge of PRRSV epidemiology in China, and may help to explain the low efficiency of MLV or killed CH-1a vaccine to protect the subgroup 1 virus infected pigs, and the great genetic diversity should be taken into consideration for control and preventive measures.