The Mediterranean Sea is a natural laboratory to address questions about the formation and evolution of continental margins and the relationship between surface and deep processes. Different regional to local events have influenced the Neogene stratigraphic evolution of the Valencia and Menorca basins. The evaporites deposited during the Messinian Salinity Crisis (MSC) strongly impact its sedimentary and geomorphological evolution. Here we present a compilation of the main regional seismic stratigraphic markers from the continental platform to the deep sea. We provide in xyz format (z in second twt) the original picking files, (not interpolated) and interpolated grid of: i) the top of the Mesozoic formation, the base of the Neogene formations including the early Miocene volcanic features, ii) the top Burdigalian, Langhian, and Serravallian seismic horizons, iii) the seismic horizons related to the Messinian Salinity Crisis, iv) the Pliocene and Pleistocene seismic horizons v) the depth of the Seafloor. The available reflection seismic dataset results from the compilation and processing of vintage seismic profiles of previous works and from the Instituto Geologico y Minero de Espana (IGME). This compilation is currently the first available in literature and provides a useful contribution to the scientific community working on sedimentary, tectonics and geodynamics within the Western Mediterranean basins.