A combined molecular and stable isotopes (C, N) investigation of the organic matter associated to the Idrija mercury deposit is being used to track the pathway of the mineralizing hydrothermal fluids and their interaction with the organic matter. The studied samples include regional barren rocks, and host rocks and ore from the mine. The Rock-Eval parameters indicate that the organic matter disseminated in regional and mine rocks is mature to post mature. The bitumens from mineralized samples are depleted in aliphatic hydrocarbons and enriched in polycyclic aromatic hydrocarbons (PAH), aromatic sulfur compounds (S-PAH) and hydrogenated PAH. The isotopic compositions of kerogens, bitumens, and individual hydrocarbons point to thermal and oxidative degradation of indigenous and migrated bitumens during mineralization and later evolution of the Idrija deposit.