Hydrothermally-altered volcano-sedimentary rocks of Eocene-Oligocene age in western Thrace, Greece, host several porphyry-epithermal deposits. The Koryfes and Konos Hill at Sapes, Pagoni Rachi, and Papadokoryfi porphyry Mo-Cu-Au- Re deposits are hosted in subvolcanic rocks of dioritic to granodioritic composition. Their central parts are dominated by potassic and sodic-calcic/potassic alteration, characterized mainly by biotite, minor K-feldspar, albite, epidote, hornblende-actinolite, chlorite, and calcite. EPMA data from both magmatic and hydrothermal biotite revealed the following results: Hydrothermal biotite from the Sapes and Pagoni Rachi areas are relatively enriched in SiO2 and MgO and thus are characterized as phlogopites, while the magmatic ones are more Fe-rich and fall close to the phlogopite-biotite transition. Fluorine, present in small amounts in the magmatic biotites (up to 1.86 wt. % F), is significantly enriched in the hydrothermal biotites, with more F-rich compositions coming from the pervasively-altered samples from Koryfes, Sapes area (up to 5.69 wt. % F). In contrast, Ti content is much lower in the hydrothermal biotites, compared to their magmatic counterparts (values up to 4.63 and 8.68 wt. % TiO2, respectively). In the Papadokoryfi area, this trend is weaker, as TiO2 depletion and SiO2-MgO enrichment is less significant as in the aforementioned areas and fluorine content does not exceed 2.05 wt. %. Chlorine is present in minor amounts (up to 0.33 wt. % Cl) and cannot be used to discriminate the two types of biotites. These mineral-chemical differentiations suggest enrichment of Si and Mg and depletion of Ti under increasing oxygen fugacity conditions, which mark the transition from the late magmatic to the hydrothermal stage. The magmatic-hydrothermal event is also characterized by a significant introduction of F, which is reflected in biotites and enhanced by the presence of topaz and zunyite in the lithocaps overlying the cores of the system at Sapes, but also due to the presence of minor fluorite in the stockwork veins, in the Pagoni Rachi area.