Experimental data concerning the effects of diagenesis and fossilization on soft-bodied microorganisms (particularly algae preserved in siliceous sediments) have been obtained through systematic monitoring of morphological and organic chemical changes in filamentous blue-green algae (Lyngbya majuscula, Oscillatoriaceae) during simulated fossilization in synthetic chert. With increasing time and temperature, there were tendencies toward reddening, darkening, and fragmentation of algal filaments, reduction in the size of algal cells and sheaths, destruction of micellar order in sheaths (with consequent loss of bire-fringent character), coalescence of trichomes, and destruction of intracellular components with preferential preservation of sheaths and cell walls. In addition, some algal filaments were damaged by growth of quartz spherulites, producing artifactual morphologies that appear to have natural counterparts in Precambrian fossiliferous cherts. Original algal hydrocarbons, and particularly normal alkanes, were relatively stable, but several previously absent hydrocarbons were produced through decomposition of other organic compounds. Isoprenoid compounds, chlorins, and probably porphyrins were derived from the degradation of algal chlorophyll. The δC13PDB value of algal carbon was unaffected in most experiments but decreased by 3‰ under extreme time and temperature conditions. Results of this study suggest trends in the morphological degradation of naturally silicified algae, demonstrate that certain morphologies are artifacts of the silicification process, and suggest possible explanations of observed organic chemical trends in recent and ancient sediments.