Abstract: The intensity and widespread of the porcine epidemic diarrhea(PED)have continuously been on the climb in Fujian since the end of 2010.The infectious disease caused high mortalities in suckling piglets,and has become one of the most serious concerns for the pig farms in the area.To deter the epidemic and understand the genetic variations of S genes of PED viruses,295 clinical samples from 117 sizable pig farms were collected during 2011-2014 for RT-PCR analysis.Overall,205 out of 295samples(69.49%)were tested positive.Annually,the infection rate declined from 87.3%,75.00%,40.91%to 34.15% during the year of 2011 to 2014.Nonetheless,it remained a serious problem for the industry.The study on nucleotide sequence revealed that the S genes of the 14 isolated PED strains shared 98.5%-100.0% homogeneity among themselves,and 93.3%-99.5% in comparison with other strains in China,93.8%-94.1% with CV777,and 95.8%-96.1% with NPPED2008_2.Variants,insertions and deletions of amino acids on the genes were found.The phylogenetic analysis on the 14 PED viruses showed a close relationship with the Thailand and Korean strains,and a remote one with the attenuated DR13 and CV777.The S gene sequence obtained from this study has been filed with Genbank.