A large, multistage program (GEothermie 2020) for developing the deep geothermal energy resources of the trans-border (Swiss- French) Greater Geneva Basin has been initiated in 2013 by the State of Geneva (Switzerland). In this framework, two PhD research projects have been initiated to study the subsurface geology of the region focus on both geothermal and hydrothermal energy prospection. The first project aims at characterizing facies distribution, petrophysical and thermal properties of the sedimentary sequence ranging from Permo-Carboniferous to Lower Cretaceous units. The second project investigates the basin structural evolution, fault-related fractures and their geometrical characteristics and properties. This information is being integrated in 3D geological models at both regional and local scale, derived from 2D seismic lines and well data. Detailed rock typing description from petrophysical measurements and laboratory analysis of core and outcrop samples (facies and micro-facies description; geochemical, petrophysical and thermal properties) are being carried out in order to assess the lateral variations of facies and their reservoir properties. Fracture analysis and laboratory test from outcrops and core data are also being performed in order to develop mechanical-stratigraphic models of target reservoir units. Regional facies mapping based on reconstruction of depositional environment evolution through time, as well as insights on structural evolution of the basin will help to understand better the distribution of productive reservoir facies and fractured zones within the study area. These elements will be key geological parameters for the successful development of geothermal energy in the Greater Geneva Basin.