In January 2004 the Life and System Biology Department of the University of Turin (Italy) started a systematic survey of the mega-fauna in the framework of the Life Project Del.Ta. NAT/IT/000163. Dataset LAMPEDUSA_2004-2006 includes 3 years of effort (survey track) and sightings data of cetaceans and marine reptiles, collected from dedicated trained Marine Mammal Observers (MMOs) on board of an inflatable boat, in the Pelagie Archipelago (Sicily Strait, Mediterranean Sea). MMOs placed on both sides of the inflatable boat collected data following random and fixed transect, each observer covering an angle of 130° from the bow, and monitoring mega-fauna presence and distribution.