Atypical porcine pestivirus (APPV) have been detected in swine herds from the USA, Germany, the Netherlands, Spain and most recently in Austria, suggesting a wide geographic distribution of this novel virus. Here, for the first time, we reported APPV infection in swine herds in China. Newborn piglets from two separate swine herds in Guangdong province were found showing typical congenital tremors in July and August 2016. RT-PCR, sequencing and phylogenetic analysis showed APPV infection occurred. Phylogenetic analysis showed that Chinese APPV strains, GD1 and GD2, formed independent branch from the USA, Germany and the Netherlands. Nucleotide identities between members of the APPV ranged between 83.1% and 83.5%, and this showed APPV is highly diverse. It is apparent that this provides the first molecular evidence of APPV infection in swine herds in China.