Fubao Bay is located in the north of Lake Dianchi, which is one of the most seriously polluted bays in the lake. Two mainrivers, Haihe River and Daqinghe River flow into Fubao Bay from the north. Four sampling sites were settled in this bay, and thesediment samples were collected by using Petersen grab. For the first time, the study of recruitment ability of Microcystis in differentsediment environments was carried out in simulation devices. The results in the present study showed that the recruitment ability ofMicrocystis was quite different depended on its habitat environments. The Microcystis recovery was inhibited in lacustrine sedimentsnear estuary, and the maximum biomass (calculated as chlorophyll-a) was pretty lower than other sampling sites. Compared amongEast Coast Area, West Coast Area and Hydraulic Mud Fill Area, the Microcystis biomass were only 4.7%, 6.6% and 11.9%,respectively. And Microcystis biomass (calculated as Microcystis cell numbers) were about 5.2%, 10.3% and 19.4%, corresponding.All the results indicated that sediments in estuary of Fubao Bay were not appropriate for Microcystis recruitment. The contribution of“seeds bank” recruiting to form HABs in this bay could be much less than the wind-induced external loading. All these results couldbe helpful in Microcystis blooms forecasting, preventing and controlling in the future.