The ‘molecular marker’ concept has its origins in the early history of organic geochemistry. In the 1930s, Alfred Treibs established the biological origin of petroleum by relating structural features of tetrapyrrole compounds in geological materials to those of photosynthetic pigments. Similarly, compounds having structures that are unique to specific pollutant sources are now commonly used in environmental organic geochemistry. For example, molecular markers are frequently used to track pollutant sources in the environment (tracers), to estimate the relative contributions of various inputs (quantitative source apportionment) and to reconstruct the depositional history of accumulating sediments (molecular stratigraphy). Information concerning the sources of such markers is contained within their structures, molecular assemblages and stable isotopic compositions. Consequently, preservation of this information is paramount. In this talk, several examples of the application of molecular markers in environmental organic geochemistry will be presented along with a prognosis for future development of these powerful tools.