This review inquired the recently applied molecular biological and biochemical methods analyzing the microbial community structure of groundwater and, as a result, summarized the functional or taxonomic groups of active microorganisms with major contaminants in groundwater. The development of gene amplification through PCR has been possible to figure out microbial population and identification. Active microbial community structures have been analyzed using a variety of fingerprinting techniques such as DGGE, SSCP, RISA, and microarray and fatty acid analyses such as PLFA and FAME, and the activity of a specific strain has been examined using FISH. Also, this review included the dominant microflora in groundwater contaminated with fuel components such as n-alkanes, BTEX, MTBE, and ethanol and chlorinated compounds such as TCE, PCE, PCB, CE, carbon tetrachloride, and chlorobenzene.