Abstract: Fluorescence in situ hybridization(FISH) has been widely applied for analyzing the composition of microbial communities in complex environmental samples.The examination and identification of individual microbial cells within their natural habitat could be performed,and those ye\|to\|be cultured microorganisms could be visualized by this technology.The information about morphology,number and spatial distribution of the microorganisms could be provided by FISH within rRNA\|targeted oligonucleotide probes or PNA.Furthermore,it is a powerful tool for studying environmental microbiology.The authors reviewed the major techniques and progresses of FISH,and its applications in microbial ecology,and subsequently discussed the perspectives of FISH.