In order to achieve consecutive and markerless modification in B.pumilus SCU11 genome and increase the production of alkaline protease, we established a markerless genetic modification system for B.pumilus based on counterselection of Upp gene, and a copy of the alkaline protease gene AprE was inserted into the 16S rDNA region in the genome of B.pumilus. The shaking flask fermentation experiment showed that the alkaline protease activity of mutant strain reached 7125 U/mL, which was 33.1% higher than that of the parental strain. The results showed that the system can achieve markerless genetic modification to the Bacillus pumilus genome, and the final screening efficiency in doublecrossover of AprE insertion strains was about 23.07%.