Cereal- legume rotation has been promoted as a strategy to increase crop yields in subsistence farms of sub Saharan Africa, and is believe d to promote changes in the rhizosphere that enhance early plant growth. This study investigates the effect of cereal-legume rotation (maize (Mz)–soybean (SB); common bean (CB)-SB-Mz; SB-Mz) in combination with different rates and types of phosphate (P) fertilizers: Minjingu phosphate rock (MPR) and Trip le super phosphate (TSP) on crop yields and total microbial diversity in a Kenyan Ferralsol. Soil sampling for analysis of microbial diversity was done in the third season of rotation, at three weeks af ter crop emergence. The microbial communities from the rhizospheric soil were genera ted using denaturing gradient gel electrophoresis (DGGE). Shannon Weaver index of diversity was used to determine the microbial diversity. Results showed significant increases in crop yields with a significant interaction (P = 0.05) between fertilizer addition and rotation regime during the three seasons. The highest maize yields were realized following a CB-SB-Mz rotation with a 150% increase (3 t /ha above the control), in plots with 50 kg P/ha MPR, while Mz-CB and SB-Mz rotation had si milar maize yields regardless of the fertilizer applied. Crop rotation and applica tion of P fertilizers had a highly significant interaction (P=0.001) and a positive impact on both total bacterial and fungal community. Significant increases in total community bacteria were noted in Mz-CB rotation system (1.48), followed by the SB-Mz (1.44) and CB-SB-Mz systems (1.42), while the total fungal diversity was significantly lower in the Mz-CB rotation (0.93), but higher in the SB-Mz system (1. 12). Overall interactions between crop rotation and P fertilizers affected the total diversity of bacterial and fungal communities in the bulk soil but crop rotation was more important in determining the total microbial diversity than the fertilizers! . There seems to be no sign