A total of 735 nasal swabs or lung tissue samples were collected from pigs on farms and in slaughterhouses in Guangxi province of southern China from 2013 to 2015, containing 55 positive samples identified by RT-PCR. Fourteen strains were successfully isolated by serial passages on MDCK cells, including 11 H1N1 and three H3N2 IAVs-S. These results indicate that different subtypes of IAVs-S co-circulating in Guangxi. The nucleotide sequences of the 14 IAVs-S determined in this study will be deposited in the GenBank database under numbers KM061010 to KM061025 and MF927789 to MF927884.