Shanzai reservoir is one of the drinking water sources to provide 0.23 million people living in Fuzhou City, Fujian province, China. There has excessive blue-green algae growth in this reservoir from 2000 especially in the warmer seasons. Many species of algae can live on sediments during conditions unsuitable for growth. This is true for most blue-green algae, some of which develop as surface water blooms, such as Anabaena and Aphanizomenon produce akinetes forming seed banks which can survive on sediments of water bodies for overwintering. Although the toxic blue-green algae Microcystis does not produce any specialized dormant cells like akinetes, it is reported that Microcystis colonies can accumulate on the sediments during autumn and winter in a vegetative state. We have addressed the question of whether the sediment provides the inoculum for Microcystis population in the eutrophic Shanzai reservoir. Our hypotheses were that if any factor might enhance recruitment of Microcystis from the sediment. Five core samples were collected from the sediment on December 2009 in the dam section of Shanzai reservoir. We examined the recruitment responses of Microcystis to the culture conditions including temperature, light intensity, pH, nutrient, physical disturbance and zooplankton in the sediment of the Shanzai Reservoir. Many kinds of Zoobenthos and algae could be found in the sediment. The main algae included Cyanobacteria, Diatom and Chlorophyta etc. The result of orthogonal experiment showed that temperature was the most important regulating factor for the Microcystis recruitment from sediments, the increased temperature would promote the recruitment of Microcystis, the second one is the light intensity. The effects of the overlying water pH, nutrient, physical disturbance and zooplankton on the recruitment of Microcystis from sediments were not obvious. Reinvasion was quantified by the diminution of benthic Microcystis abundance, and moreover, by the increase of Microcystis in the water column. Our results from the laboratory experiment suggest that the Microcystis in the sediment could recruit and float up to the water surface which support our hypothesis that the sediment is the important seed banks and provide the inocula for Microcystis blooms in Shazai Reservoir and temperature was the most significant environmental factor regulating the recruitment of Microcystis from the sediment. The results would provide a scientific reference for controlling Microcystis bloom in the Shanzai reservoir.