Abstract: To fully understand the knowledge of variant porcine reproductive and respiratory syndrome virus (PRRSV) genetic variation and pathogenicity, the ORF5 and NSP2 genomes of PRRSV-FJ09A strain were amplified by RT-PCR and sequenced. Comparing with PRRSV-VR2332, ORF5 gene shared 87.6%of nucleotide homologies and 88.1% of the deduced amino acid homologies, there were point mutations within deduced amino acids, focus on amino acids of associated with virulence, epitope and N-glycosylation sites;NSP2 gene shared 80.9% of nucleotide homologies and 77.0% of the deduced amino acid homologies, and it shared a common feature of 31 amino acids deletion in three places which one place more of a phenylalanine(F) than other local reports. Comparing these sequences with Chinese PRRSV strains published after 2006,ORF5 gene shared 98.5%-99.7% of nucleotide homologies and 97.5%-99.5% of the deduced amino acid homologies, NSP2 gene shared 98.4%-99.3% of nucleotide homologies and 97.3%-98.9% of the deduced amino acid homologies. The phylogeneic tree revealed PRRSV-FJ09A strain isolated had closer relationship with PRRSV-FJ06A strain. According to the animal experiment PRRSV-FJ09A had a high pathogenicity to 30 d pigs.