Intact polar membrane lipids (IPLs) can serve as chemical biomarkers of living cells that can provide information on the extant microbial community structure and in situ microbial processes. IPLs analysis is a culture independent, rapid and non-selective procedure in contrast to biological methods. The compositions of cell membrane intact polar membrane lipids of bacteria and Achaea and their applications in the researches of biogeochemistry and microbial ecology are summarized in this paper. The recent progresses of IPLs applications are reviewed, with emphasis on those microorganisms that play a specific role in biogeochemical cycle, such as anaerobic ammonium-oxidizing bacteria, anaerobic methanotrophic Achaea, ammonia-oxidizing Achaea and marine Crenarcheota with tetraether lipids, or those special ecological systems, such as hydrothermal vent, cold seep and marine deep biosphere. The advances of analytical method for microbial IPLs in marine sediments are briefly introduced, and their application prospects are proposed.