Abstract: In order to monitor the variation of highly pathogenic porcine reproductive and respiratory virus (PRRSV) prevailing in recent years, the complete genome of a strain of PRRSV SD0901 isolated from one pig farm with clinical outbreak of PRRS was sequenced and analyzed by RTPCR amplification. The results showed that the genome size of the virus was 15 230 nucleotides, excluding the poly (A) tail. Comparative analysis of the whole genomic sequences revealed that the virus shared 98.6%98.7% identity with the representative strains of highly pathogenic PRRSV, and exhibited additional one amino acid deletion and insertion at the position 468 and 585586 respectively, besides 30amino acid deletion within its Nsp2coding region. In addition, one amino acid variation was found in GP2, GP3, GP4 and Mcoding regions of its genome, respectively. Phylogenetic analysis showed that the virus formed an individual branch although it belonged to the same subgroup as highly pathogenic PRRSV strains. These findings indicate that the virus is a variant of highly pathogenic PRRSV, implying that the variation of highly pathogenic PRRSV have occurred during its prevailing. Our study provides valuable genomic data for monitoring and analyzing genetic variation and evolution of highly pathogenic PRRSV.