Thapsos is a settlement located on the Magnisi peninsula, a triangular strip of land between the gulfs of Syracuse and Augusta. Here it developed a remarkable Middle Bronze Culture (1440-1250 BC), with a village with proto-urban character for the influence of import and know-how from the Aegean, Cyprus and Malta. The necropoleis of Thapsos are arranged in 3 areas of the peninsula. For our analysis we considered the two groups of rectangular shaft tombs with underground chamber necropolis, widespread on the limestone plateau to the North and South of the peninsula. A first partial study about the orientation of the Thapsos’ shaft tombs was realized at the beginning of the third millennium on 25 tombs in the North necropolis; in this first analysis it was observed that there were two privileged orientations: one of astronomical character, linked to the sunrise at the summer solstice, and the other of topographical character, connected to Mount Etna (North direction). The new archaeoastronomical analysis on the Thapsos’ shaft tombs was started by the authors in 2016 and involved 70 tombs located on the peninsula. The opportunity to study the orientations of these tombs allowed to realize the first mapping of the necropoleis and the numbering of the tombs. The proposed study is therefore of great scientific importance, as it was previously thought that in the Bronze Age had lost cultic tradition of building shaft tombs necropoleis with astronomically oriented entrance. The study thus opens new scenarios as part of the funerary rituals and religious needs, showing a discontinuity with the previous phases.