Abstract: To investigate the proteinvariationsin the porcine epidemic diarrhea virus(PEDV),19 Eand 18 M genes from the viruses collected from different farms in Fujian in 2012-2014 were cloned and sequenced.The results indicated that the PEDVEand Mgenes were conservative.There were individual variants foundonlyonamino acids,as compared with CV777 strain.On the nucleotide sequences,the E geneswere 97.4%-100.0% homogenous among themselves,97.4%-100.0% homogenous with attenuated DR13 strain,and 97.0%-99.6% homogenous with CV777 strain.For the M genes,they were 97.4%-100.0% homogenous among the 18 of them,97.2%-99.6% homogenous with attenuated DR13,and 97.5%-98.4% homogenous with CV777.A phylogenetic analysis indicated that the Egenes of the 19 PEDVs were closely related to CV777,and the Mgenes of the 18 PEDVs closely related to KU05CB08.The M gene wasa new variant,which might bear an origin of strains from Thailand.