The intestinal microbial composition of fish is closely related to their living environment. In order to investigate the origin of of Coilia nasus and Coilia brachygnathus in Poyang Lake， samples were collected from the the main stream of the Yangtze River， Poyang Lake， the Qingcaosha Reservoir in the Yangtze Estuary and the sea area of Shengsi in different months. The intestinal microorganisms of the samples were comparatively analyzed using 16S rRNA high-throughput sequencing technology.The results showed：（1） among the different sampling groups of C. nasus， the abundance of intestinal microorganisms of the samples from the section of Pengze in March was significantly higher than that of the samples from Poyang Lake， Qingcaosha and Shengsi. The richness of intestinal microorganisms of one group from the in Poyang Lake （PC-4） in April and one group from Qingcaosha had a high similarity with those of the samples from Shengsi （SC-3） through PCoA， suggesting that they may migrate from Shengsi. （2） The intestinal flora of Coilia brachygnathus varied greatly in different regions， while the differences between different months in the same region were smaller. But the intestinal flora in Poyang Lake in May was significantly different from the other sampling groups， indicating that they might have migrated from different places. （3） The average abundance and diversity of the intestinal flora of Coilia brachygnathus in Poyang Lake were higher than those of Coilia nasus in Poyang Lake. The above results demanstrated that there may be migratory populations of both Coilia nasus and Coilia brachygnathus in Poyang Lake.