Recruitment of Microcystis dormant from the upper sediment is a critical stage in its life history and plays an important role in forming blooms. However, little is known about the benthic bacteria associated with recruitment of Microcystis cells in sediment. To investigate the relationship between the recruitment of dormant Microcystis and bacterial flora in the upper sediment, we detected and comparatively analyzed the density of bacteria and the abundance of Microcystis dormant in the upper sediment in Lake ChongTian, situated to the west of Lake DongTong, where Microcystis blooms have formed frequently in recent years. At the same time, bacterial density,the abundance of Microcystis cells, and some of the physical and chemical properties of the overlying water column were measured. Results show that total bacterial density in both the upper sediment and the overlying water column gradually increased from January to May, remained stable from June to September, and decreased gradually from October to December. However, the total bacteria density in sediment was significantly higher than that in the overlying water column in each month. From April to June, total bacterial density significantly increased (P < 0.05) and the density of dormant Microcystis significantly decreased (P < 0.05) in the upper sediment, which indicated that the recruitment of dormant Microcystis began in April. In the same period, the concentration of dissolved oxygen (DO) and the TN/TP ratio decreased significantly in the overlying water column. In May, the total bacterial density in sediment was 7.32×10⁵ colony-forming units (cfu)/mL, significantly higher than that in April; moreover, the proportion of dominant flora increased remarkably(up to 61%). The density of Microcystis cells in the overlying water column increased significantly to 180×10⁶ cells/mL in June, and Microcystis aeruginosa was dominant the Microcystis species.The density of dormant Microcystisin the upper sediment reduced to its minimum value,3.71×10⁶cells/mL, at this time. In July, the total bacterial density in the upper sediment was not significantly different from that in May and June, and the proportion of dominant flora decreased to 40%-42%, which was the average value in other months. Meanwhile, the density of Microcystis cells in the overlying water column decreased significantly, and the density of dormant Microcystis increased significantly in the upper sediment (P < 0.05). In August, the total bacterial density in the upper sediment was 8.89×10⁵cfu/mL,which was the highest value for all months, and the proportion of dominant flora increased significantly (up to 57%). Consequently, in September, the density of dormant Microcystis in the upper sediment again decreased significantly; in contrast, the density of Microcystis cells in the overlying water column increased significantly (P < 0.05). This study also revealed that the dominant Microcystis species in Lake ChongTianwere M.aeruginosa, M.flos-aqua, and M.wesenbergii, though the relative proportions of these species differed in different months. The dominant bacterial flora in the sediment and overlying water column were Exiguobacterium, Pseudomonas,and Bacillus,all of which can promote, to some extent, the recruitment of dormant M.aeruginosa, M.flos-aqua,and M.wesenbergii from the upper sediment. These results have important implications in that dominant bacterial flora in the upper sediment may exert important effects on the recruitment of dormant Microcystis species from the upper sediment.