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Results of the current and already published studies suggest that the Tortonian in age deposits could serve a major source rocks (for both oil and gas) beneath the Messinian evaporites in the Hellenic trench system. Additionally, the strong terrestrial input in Pliocene deposits could lead to the production of biogenic gas, similar to the Po basin in Adriatic Sea (Italy). In the current study, fourteen samples from late Miocene Faneromeni section and twelve samples from the early Pliocene Makrilia section in eastern Crete were collected in order to evaluate their hydrocarbon generation potential. For this purpose, Rock-Eval analysis and characterization of the organic matter were performed. The results document a clear distinction between the two sections. Faneromeni section contains organic matter of kerogen type III, whereas the Makrilia section contains organic matter of kerogen type IV. The HI/TOC plot diagram, in both sections, indicates poor oil generating potential, with the exception of several samples showing fair to good gas and oil potential. Although thermal maturities of the samples from the two successions are similar, according to the Tmax values, samples from Faneromeni succession exhibit higher hydrogen index values, indicating a better quality of organic matter in terms of hydrocarbon generation. Very low obtained concentrations of bitumen (mg/g of rock), as well as the predominance of NSO compounds, compared to the saturates and aromatics, indicate low maturation level. The n-alkanes profiles exhibit a bimodal distribution, indicating a mixed origin (marine and terrestrial) of the organic matter in both areas. Terrestrial organic matter input is more pronounced in Makrilia section. The analysis of saturated biomarkers indicates that Faneromeni deposits were accumulated under constant organic matter input in an environment influenced by cyclic changes (from marine to lagoon origin and vice versa). Faneromeni section corresponds to a restricted basin during Tortonian, with quick and often sea-level fluctuations just before the Messinian crisis, while Makrilia section represents a very restricted intramontane basin with strong terrestrial influence. © 2015, Springer-Verlag Berlin Heidelberg.