—We present results of study of the chemical composition of organic matter (C, H, N, and S) from Holocene sections of lake sapropels with undisturbed stratification penetrated by vibratory drilling of the bottom sediments, down to the underlying rocks, of Lakes Bol’shie Toroki (1.8 m), Minzelinskoe (5 m), Ochki (4.5 m), Dukhovoe (7 m), and Kotokel’ (6 m). We consider methodological approaches to the identification of the sources and genesis of buried organic matter in marine and lacustrine sediments by a number of organogeochemical indicators: data of a biological analysis (biostratification based on layer-by-layer determination of organic relics in bottom sediment sections); hydrocarbon biomarkers (molecular composition of normal aliphatic hydrocarbons (n-alkanes), nitrogen compounds of a protein complex, etc.); and C/N ratio reflecting a difference in the biochemical compositions of bioproducers. The results of biological analysis (biostratification) show that planktonogenic sapropel (phyto- and zooplankton, the autochthonous source of organic matter) in Lake Ochki formed for 10,760 years, and sphagnum and hypnum moss were supplied from the bogged shores (allochthonous source of organic matter). In Lake Minzelinskoe, peaty sapropel formed at the stage of a flooded lowland bog (5905 years ago); since 3980 years ago and till the present, macrophytogenic sapropel has formed. Pyrolytic study (RE pyrolysis and Pyr–GC–MS analysis) of bioproducers and sapropel from Lake Ochki has shown that phytoplankton and zooplankton were the main autochthonous source of OM in the lake, which is confirmed by the identified macromolecules of nitrogen compounds of different compositions. The presence of hopanes indicates the contribution of microorganisms to the formation of OM in the sediments. The organic matter of sapropel has a terrigenous component, which is confirmed by the presence of high-molecular odd-numbered n-alkanes, ketones, and methyl esters of fatty acid. The C/N ratios in the stratified sections of macrophytogenic sapropels of Lakes Bol’shie Toroki and Minzelinskoe fall in the range of values specific to higher aquatic and terrestrial vegetation (C/N = 15–18), whereas the C/N ratios in planktonogenic sapropel of Lake Dukhovoe are typical of marine and lake plankton (C/N = 5.7–8.6).