Abstract: In this paper, three main methods for studying soil microbial diversity ［biolog analysis, phospholipid fatty acid analysis (PLFA) and nucleic acid-based analysis］ are briefly introduced and their advantages and disadvantages are evaluated. Fertilization-associated alteration in soil properties would have long-lasting effects on soil microbial community and the effects would depend on fertilization rates and fertilizer types. The response of soil microbial diversity and overall biological activities to tillage can be variable and will depend on other factors such as the cropping and abundance of residues. Under most experiment conditions, conservation tillage practices (i.e. no till with mulch) can potential increase soil microbial diversity and biomass compared to conventional tillage. Based on recent related research, perspectives for studying microbial diversity in soils are also presented.