Seismic reflection profiles from the marine areas around Santorini in the south Aegean arc show the distribution of active faults and the occurrence of submarine volcanic rocks interfingering with stratified basinal sediment. Santorini is located at the intersection of fault sets of different ages. To the west, active faults trend east-west, whereas to the east, active faults trend ENE-WSW and a slightly older set of faults trends NE-SW. Subsurface submarine volcanic rocks can be dated using ages estimated for the stratified basin sediments elsewhere in the Milos-Christiani Basin. Volcanic horizons off Santorini correlate with the main (young) Akrotiri (0.65-0.55 Ma) and old Akrotiri (1.6 ka) volcanic episodes, respectively. Off Christiani, the upper unit of volcanic rocks is of similar age to the young Akrotiri episode and the lower volcanic unit is likely to be of latest Pliocene age. Late Neogene basin subsidence and volcanism are a consequence of changing patterns of faulting resulting from the collision of the African and Aegean-Anatolian plates.