Various facies characterize the Lower Eocene (Ypresian) that had been named formations which include the Bou Dabbous Formation. It is one of the four lateral equivalents of the Metlaoui Group and consists of micrite and marls with abundant planktonic foraminifera (Globigerina). In this paper, we report on the organic matter (OM) analyses of the Bou Dabbous Formation from nine outcrop cross sections in central and northern Tunisia. The total organic carbon (TOC) values and Rock-Eval analysis showed that this formation had preserved type II/III marine OM. Locally, such as at Oueds Sidi Mansour and Bou Jabia, TOC values are very high. These values are reliable to the structural framework (subsiding grabens) during the deposition of the Bou Dabbous Formation. Biomarker (steranes and terpanes) analysis showed that this OM is very rich in these compounds. Our results exposed that the Bou Dabbous Formation OM is represented by an open planctonic to estuarine algal facies with bacterial contribution as revealed by the relative abundance of the C27 (37–43 %), C28 (26–31 %), and C29 (30–34 %) steranes and the dominance of the hopane compounds for all the samples. The good preservation of OM in the Bou Dabbous Formation has been evidenced by the high abundance of gammacerane and the preservation of the C34 and C35 homohopanes in central Tunisia (Oueds Souinia and Sidi Mansour) compared to the northern part (Tellian Atlas). We interpreted that the development of anoxic conditions in central Tunisia had been induced by water stratification of super-salt water under arid and warm climate. These results concord with the structural and the paleogeographic setting where the Bou Dabbous Formation in central Tunisia was deposited in subsiding grabens separated from the open sea by high sills (horst). In northern Tunisia, eastern upwelling waters rich nutriments enhanced primary organic productivity and therefore the development of anoxic conditions. Rock-Eval maximum pyrolysis temperature (T max) values fitting with the interval 425–454 °C show that the OM thermal maturity ranges from immature (central Tunisia), marginally mature (Bizerte region) to the peak of oil generation window (NW Tunisia). We showed that these thermal maturity differentiations were related to the geodynamic evolution that had gone separately central and northern Tunisia. Therefore, the Bou Dabbous formation in central Tunisia had gone subsidence inversion and tendencies to emersion since the Late Eocene epoch and consequently not enough to reach the oil generation window. On the other hand, at the Oligocene–Early Miocene, extensional activity favored dissymmetric subsidence where northern Tunisia (Tellian Atlas) had gone active subsidence associated with high thermal flux in relationship to magmatic activities. Consequently, this feature explains the thermal maturation of the Bou Dabbous OM at this province.