We present new results on catagenetic alteration of dispersed organic matter (DOM) and individual hydrocarbon composition of bitumen extracts from the lower mesocatagenesis and apocatagenesis zone, based on the study of core samples from superdeep well SV-27 (Vilui syneclise), which penetrated Permian and Upper Carboniferous coal-bearing strata. The vitrinite reflectance data show a progressive increase in the thermal maturity of DOM at a depth of ~4 km. The major biomarker indicators of the thermal history of DOM in the central part of the Vilyui syneclise appear to play only a minor role below this depth, thus reflecting the early stages of mesocatagenesis. The pristane/phytane ratios begin to invert at the same depth. Bitumen extracts from core samples collected from this depth contain new hydrocarbons in trace amounts, which increase with depth. The identified compounds include homologous series of alkenes, 2,4- and 2,7-dimethylalkanes, and alkylcyclohexanes with a prevalence of compounds with an odd carbon number predominance. Unusual differentiation of aliphatic and cyclic hydrocarbons with even and odd carbon-numbered chains occurs at the maximum depth (6458 m). Among aromatic hydrocarbons, four new diastereomers are identified: 17-desmethyl–23-methylmonoaromatic steroids C27. Considerable variations in the composition of bitumen extracts from the apocatagenetically altered core samples appear to reflect the termination of hydrocarbon generation from kerogen and further thermolysis of residual bitumens, including their asphaltene components. This explains the low values of maturity biomarker indicators corresponding to the apocatagenesis grade, since in this case they reflect the composition of hydrocarbons generated during the early stages and later occluded and adsorbed by asphaltenes. “Deep-seated” microoil from Permian, Carboniferous, and Cambrian deposits did not participate in the formation of oil rims and major gas condensate pools in the Vilyui petroleum area.