Recently, microbial ecology and related phenomena of seafloor hydrothermal vents have been the focus of geomicrobiology. Discoveries from these extreme environments continue to challenge accepted notions about microbial metabolism, limits of life and elemental geochemical cycles. Compared with traditional cultivation, phylogenetic analyses based on the small subunit rRNA (16S rRNA) and certain diagnostic metabolic genes have provided systematic and comprehensive methods to study microbial communities inhabited in hydrothermal chimneys. Cultivation-independent molecular techniques include construction of gene library, DGGE, T-RFLP, FISH and quantitative PCR. At present, these approaches have been successfully applied into the studies of geomicrobiology in global seafloor hydrothermal vents. Moreover, lots of achievements have also been accomplished in the investigations of microbial diversity, processes of key element geochemical cycles involved with microbes, the interactions between microbes and minerals, the origin of life and their evolution. In this review, we briefly outline the principles of various methods and their applications in research of microbial ecology of hydrothermal vents.