Nitrogen (N) fixing Klebsiella pneumoniae RSN19 has high inorganic phosphorus (P) solubilizing capability, but its N2-fixing capability is limited. In order to acquire a P-solubilizing mutant strain with high efficiency N-fixing capability, different microwave irradiation intensities and durations were tested on RSN19 in an attempt to produce mutants with improved N2-fixation and P-solubilization capabilities. The effect of microwave irradiation power and time were studied and the microwave mutagenesis parameters were optimized. Nitrogenase activity was tested on the mutant strains by acetylene reduction method; and their P-solubilizing capability and genetic stability were determined. The results indicated that the best conditions for microwave mutagenesis that produced better performed mutant strains were 250W, 36 s. Under these conditions a maximum positive mutation rate of 1.66% was obtained, resulting in five genetically stable strains with promoted nitrogenase activity which was designated as RSM-219, RSM-206, RSM-224, RSM-225 and RSM-275. Subculture tests showed that RSM-219 and RSM-206 were genetically stable mutant strains with higher nitrogenase activity and phosphate solubilizing capabilities than the original strain. Both RSM-219 and RSM-206 performed better than the original strain under N-free conditions when supplied with calcium phosphate only, and produced greater increases in the biomass of alfalfa seedlings.