Molecular markers are organic substances that carry information about sources of organic matter or contamination. The source/marker relation can be used to indicate the presence of a given source material (qualitative), or, under appropriate conditions, to estimate the amount of a source material (quantitative source apportionment) in the environment. Assemblages of markers can also be used as process probes. In this instance, systematic differences and/or similarities in the physical-chemical properties of markers are coupled with compositional changes in marker composition to infer the operation of natural processes. This paper provides an overview of what molecular markers are, what types of markers are present in the environment, the requirements for the use of markers, and some common applications. To illustrate how molecular markers can answer specific environmental questions, three case studies are presented. The first case study examines the impact of municipal waste on a large urban harbor (Boston Harbor). Linear alkylbenzenes (unreacted residues of linear alkylbenzenesulfonate surfactants) and coprostanol (a fecal indicator) provide information on the sources and likely transport pathways of municipal wastes in a complex hydrologic system. The marker data are also used to estimate the proportion of sewage-derived poly chlorinated biphenyls (PCBs) in polluted harbor sediments. The second case study concerns a portion of the continental shelf off southern California (Palos Verdes) where discharge of municipal wastewaters has led to extensive contamination of sediments and biota. Long-chain alkylbenzenes (surfactant residues), PCBs and the pesticide, DDT (dichlorodiphenyltrichloroethane), are used to develop sedimentation rate estimates for several time periods by molecular stratigraphy. These results, when combined with other information, allow conclusions to be drawn about the most likely transport pathway of sediments at the study site and to predict the fate of historically deposited contaminants. Finally, an investigation of a crude-oil spill in Bemidji, MN illustrates how monoaromatic hydrocarbons can be exploited as process probes, providing insights into the relative importance of different attenuation processes in a contaminated aquifer. The results show that natural attenuation of the monoaromatic hydrocarbons is occurring at this site and is dominated, not by physical and/or chemical processes, but by biodegradation.