The biomass from which hydrocarbons were formed and the organisms responsible for its production are usually deduced by the use of biochemical markers. In the present study, using a simulated sedimentary system, cyanobacterial organic matter was buried in sediments and exposed to sequential environmental changes ranging from microaerobic conditions at ambient temperature to strongly reducing conditions at a biologically extreme temperature and pressure. Significant changes occurred in the composition of hydrocarbons and fatty acids isolated from the biomass that masked the characteristic patterns exhibited by the original cyanobacterial material. The changes depended on the particular environmental conditions to which the organic matter was exposed. The results stress the need for caution in interpreting biochemical markers in terms of their source material in sediments.