Isoprenoid quinones are lipid molecules present id all species of respiratory and photosynthetic microorganisms and exhibit marked structural variations depending upon the microbial taxon. Taking advantage of this, quinones have been used not only as chemotaxonomic markers in microbial systematics but also as good measures of microbial populations in the environment in terms of quantity, quality, and activity. Basically, this biomarker approach, called the quinone profile method, is applicable to all environmental samples from which an absolute amount of microbial biomass greater than or equal to 10(9) cells can be collected. The quinone profile method allows good measurement of both fundamental and applied aspects of ecological and environmental microbiology. In particular, numerical cluster analyses of quinone profiles are useful for monitoring microbial population shifts in an ecosystem which is not amenable to conventional culture methods and molecular techniques. The combined use of molecular techniques and the quinone profile method in this research area should provide more accurate and reliable data regarding population dynamics and community structures.