A novel avian influenza A (H7N9) virus has caused epidemics during 2013 to 2014, and sporadic infections in 2015. To investigate the evolutionary history and seasonal variations of H7N9 in live poultry markets (LPMs), 2 655 pharyngeal swabs of chickens and ducks were collected from July to December 2013 in Suzhou, Jiangsu Province, China, which was one of the major epidemic areas in 2013. The results showed that the positive rate in winter was higher than that in summer and there were mixed infections among H5, H7, and H9 strains, suggesting the occurrence of multiple reassortment events. The HA, NA and PB2 genes from selected H7N9-positive samples were then sequenced to trace the evolutionary history of the novel H7N9 virus. Phylogenetic analysis revealed that all Suzhou isolates in this study were clustered around the novel H7N9 virus, but they also continued to evolve while circulating in the poultry. In fact, the PB2 gene of some sequenced samples was closely related to H5N1. This study identifies the genetic reassortment of a novel H7N9 virus in Suzhou and suggests that constant surveillance of all avian influenza virus subtypes in LPMs will help to track the source of newly emerging virulent viral strains.