Organic matter of Cretaceous and Cenozoic deposits in the Indigirka–Zyryanka basin was studied by bituminological analysis and chromato-mass spectrometry. The regularities of distribution of alkanes and polycyclic aromatic hydrocarbons depending on the catagenesis of fossil organic matter are shown. Sesquiterpanes of the drimane series have been recognized in the Cretaceous deposits, and tetracyclic biomarkers of phyllocladane (kaurane), in the Cenozoic ones. The biomarkers were produced from terpenes of conifers, and the identified set of pentacyclic oleanenes are the products of angiosperms flourishing in the Paleogene and Neogene. As evidenced from geochemical indices, the Cenozoic deposits did not reach the PT-conditions of “the main oil formation (oil window) zone” and should not be used for the quantitative evaluation of the regional petroleum potential. Nevertheless, the Cenozoic clayey units can be perfect isolating horizons for fluids migrating from more ancient, including Cretaceous, deposits.