【Objective】To analyze the genetic variation of foot-and-mouth disease virus (FMDV) in Guangdong area, and provide fundamental data for studying FMDV infections as well as prevention and control of foot-and-mouth disease.【Method】We amplified and sequenced VP1 and 3A genes of FMDV from pathological samples of pigs in Guangdong area from 2015 to 2016, and analyzed the gene sequences.【Result】Eleven strains of type O FMDV strains belonged to the social spectrum type strains. Seven type A FMDV strains belonged to the Asia type strains. Comparing the VP1 genes of the 11 type O FMDV strains with pandemic strains, GD-MM-3 and O/BY/CHA/2010 strains had the highest sequence similarity being 95.3%, while strain GD-1, GD-MM-1 and GD-MM-3 had the highest sequence similarity of 90.8% compared to strain O/MYA/1/98. Comparing the VP1 genes of 7 type A FMDV strains with pandemic strains, A/GDMM/2013 and GD-CH-3 strains had the highest sequence similarity being 99.8%, while A/HuBWH/2009 and GD-3 strains had the highest sequence similarity being 91.4%. Amino acid deletion was not found in 3A proteins of 11 type O FMDV strains. The 3A proteins of 7 type A FMDV strains had multiple amino acid deletions.【Conclusion】The genetypes of FMDV in part area of Guangdong are complex, which leads to the difficulties of disease prevention and control.