Porcine epidemic diarrhea virus (PEDV) infection, which causes acute diarrhea and dehydration in suckling piglets, has become a serious problem for the swine industry of China in recent years. In this study, a virulent PEDV strain, GD-1, was obtained from fecal samples from suckling piglets that suffered from severe diarrhea in 2011 in Guangdong, China. Here we describe the complete genome sequence of strain GD-1, which may be helpful in further understanding the molecular epidemiology and genetic diversity of PEDV field isolates in China.