During their migratory journey en route to Africa, European birds face a barrier: the Mediterranean Sea. Differently from the majority of birds, Accipitriformes use mostly soaring-gliding flight rather than powered flight. For this reason many species of raptors tend to avoid the water-crossing by following land masses. Different degrees in dependence on soaring flight are shown by different species of raptors. In this paper, we compare the migration of Western Marsh Harriers and juvenile European Honey Buzzards by the means of simultaneous observations at two sites: Mount Olympus (northern Greece) and the island of Antikythira (southern Greece). Differences in migration timing, water-crossing behaviour, sex and age classes (in the case of Western Marsh Harriers), show that these species use different migration strategies when crossing the Mediterranean region in autumn. Western Marsh Harriers migrate through parallel fly-ways, while juvenile European Honey Buzzards migrate island hopping being attracted by landmarks and following leading lines of land masses. A simulation process demonstrated marked differences in the energy consumption rates between the two species, highlighting that the powered flapping flight is particularly more disadvantageous for the European Honey Buzzard rather than for the Western Marsh Harrier. In this case, the morphological features of the studied species could explain the existence of two different migration strategies.