Objective To investigate the seasonal variation and geographical distribution of different fly species in downtown Shanghai. Methods Conducted fly surveillance during March to November of 2013 in 2 parks and 1 residential area in Huangpu district, and then did identification and classification. Results The fly density in park environment was significantly higher than residential environment (Z=-2.870, P=0.002). Although shared the same dominant family of Calliphoridae, the flies species compositions were different between the 2 kinds of environments, Chrysomya megacephala was the predominant fly species in parks (composition ratio is 23.43%) and Lucilia sericata was the predominant one in residential (composition ratio is 20.11%). Different fly species showed different seasonal peaks and distribution trends, C. megacephala and Lucilia (s. str.) illustris had the unimodal trend,while L. sericata, Aldrichina grahami and Fannia prisca showed the bimodal trend. Conclusion The study suggests the work of fly prevention and control in downtown Shanghai should focus on the predominant Calliphoridae, such as genera of Lucilia and Chrysomya.