In order to gain insights on the genome-wide recombination in bacteria, we crossed Bacillus strains using protoplast fusion. The recombinant progenies shared the majority of the genomic regions with one of the parents . Computational analyses suggested that this biased recombination might be due to the restriction-modification systems and the genomic parameters such as GC content and local nucleotide diversity had no effect on the recombination events. Our study has great potential for improving cellular functions and better understanding of bacterial evolution.