Objective To study the molecular prevalence of the porcine peproductive and respiratory syndrome virus (PRRSV) strain in small and medium-sized pig farms of Fujian province in 2017.Method We collected 83 suspected blue ear positive disease materials from small and medium-sized pig farms in Fujian province. RT-PCR detection and genetic evolution analysis of ORF5 gene which encoded GP5 protein was performed.Result The positive rate of 83 suspected blue ear disease samples was 73%, and the nucleotide similarity among the measured ORF5 sequences was 80.3%-100.0%. The nucleotide similarities between tested strains of different branches and the representative strains of those branches, NADC30, GM2 and JXA1, were 92.6%-93.9%, 89.8%-93.0% and 93.4%-99.3%, respectively. The new identified strain in the new branch had nucleotide similarity of 91.0%-93.0% to JXA1. The GP5 amino acid alignment showed significant variation in functional regions such as GP5 signal peptide region, induction epitope, principal neutralizing epitope and hypervariable region in different subgroups.Conclusion A new branch of PRRSV has emerged in Fujian area, making the PRRSV variants in Fujian more diverse. It is necessary to strengthen the monitoring of PRRSV epidemics and mutations.