Afro-Palearctic migrants move between breeding and wintering grounds along flyways determined by several factors (bird morphology, geography, behavioural adaptations) and raptors often concentrate at straits to avoid long sea crossings. Here we test the hypothesis that raptor passages across different areas of the Turkish straits are similar in species composition as well as flight behaviour. We made simultaneous observations at the Bosphorus and at the Dardanelles in autumn 2010. We tested the influence of weather, time of day and flock size on the intensity and spatial shift of migratory flow as well as the tendency to cross the Dardanelles Strait rather than follow the peninsula. We also collected information of the flight altitude of raptors using an optical range finder. The species composition observed at the two sites was completely different, with eagles predominating at the Bosphorus and small and medium-sized raptors predominating at the Dardanelles Strait. Compensation for wind drift at the Bosphorus was species-specific, with small and medium-sized raptors showing a drift effect by crosswinds, and eagles showing compensation and overcompensation. Mean flight altitude was similar among species, while the response to weather conditions varied, being mainly affected by wind. In the case of Short-toed Snake-eagles, flight ability and response to weather conditions was also age-dependent. These results show that the flight strategies of migrating raptors are species-specific even if some flight parameters may converge as a result of risk minimisation. The differences between species and flyways probably reflect interspecific differences in the ability to fly over water.