The biogenic genesis of petroleum hydrocarbons was considered in terms of systems analysis using results on petrology of organic matter (OM), the dynamics of its catagenetic transformations in the subsurface, and experimental data on the thermolysis of natural organic matter of different origins with the detection of redistribution of X-ray phases and investigation into the formation kinetics of liquid products. The yield of petroleum hydrocarbons is due to the presence of the polynaphthene phase in the initial OM, and the group and molecular compositions of petroleum are determined by the type of initial OM, the level of its metamorphism according to X-ray or petrographic classification, and thermobaric conditions of thermolysis of organic substance in the subsurface. The polynaphthenic phase is considered as the main source of alkane, alkane-naphthenic, and naphthenic oils, whereas the analogous phase of humic OM probably produces naphthene-aromatic and aromatic oils.