The authors investigated the effect of Bacillus mucilaginosus on weathering of phosphorite. Analysis of different proteins was of significance in exploring the molecular biological mechanism in the bacterial weathering process. The concrete methods are described as follows: Mineral powder was put into liquid culture medium and B. mucilaginosus was incubated in the medium. The control (group) had no mineral powder in the medium. The treatments and controls were cultured simultaneously under the same condition. In a few days, the supernatant was filtrated, the main cations (Ca2+, Mg2+, Na+, Mn2+, Al3+, Fe3+, K+) were measured by ICP-OES, and the contents of water soluble phosphorus (Pws) and silicon (Siws) were determined by colorimetry. The residual solid was weighed on the filter paper, followed by digestion with concentrated HNO3. The concentrations of the main cations and Pws, Siws in the digest liquid were measured by using the method mentioned above. After the supernatant was centrifuged, the precipitation was used to analyze the protein differences between the treatment groups and the control groups by 2-dimentional gel electrophoresis (2-DE). The experimental results showed that apatite and quartz were partially weathered, but kaolinite was dissolved completely. The population of bacteria increased when mineral powder was added in the liquid medium. Software analysis and comparison of the 2-DE pictures of bacterial proteins revealed 1134 visible protein spots in the treatment group, and 729 visible protein spots in the control group. To compare the bacterial protein expression contents of the treatment group with those of the control group, there were 496 different protein spots, including 214 protein spots which indicated that the protein contents increased, 75 protein spots were indicative of a decrease, and 207 proteins were newly synthesized. It is proposed that the increased bacterial contents may be related to some protein expression and activation after the input of mineral powder. Newly synthesized proteins, the increase of expression contents and the reduction of proteins may be connected with bacterial metabolic regulations, cell activation and signal transmission.