Bacillus subtilis has been a model organism for gram-positive bacteria and has played important roles in metabolic engineering and industrial microbiology. Genetic manipulation technologies in Bacillus subtilis are critical for investigation of gene functions and modulation of bacteria physiologies in post-genomic era. In this review, we firstly summarize commonly used counter-selection markers for marker-free genetic manipulation. Then, we describe and compare different marker-free genetic manipulation strategies. Finally, we discuss challenges and future trends for developing more efficient tools for genetic manipulation of Bacillus subtilis.