It has been shown that deep biodegradation of the components of oils with the change in the molecular composition of aliphatic, naphthenic, and aromatic hydrocarbons (HCs) occurs upon the biodegradation of Ashal'chinskoe crude petroleum by indigenous soil microflora under laboratory conditions. It has been found that alkanes and tri- and tetracyclic aromatic HCs are present in the oils of the biodegraded petroleum not only in the molecular form but also in the form of structural fragments linked through ether or sulfide bridges in the composition of complex high-molecular-weight entities. The composition of O- and S-linked compounds of the aforementioned types is different in the oils of the petroleum subjected to biodegradation.