Populations at the far edges of their ranges tend to be scarce, and they are frequently of conservation concern. This paper examines the distribution of three raptors (Circaetus gallicus, Hieraaetus pennatus and Milvus migrans) at the southwestern boundary of their breeding range. We modelled species distribution to obtain habitat suitability indexes that were validated with extensive fieldwork in Morocco and Spain. Our results support a strong effect of habitat suitability and a bottleneck effect of the Strait of Gibraltar on raptor distribution. However, after controlling for these effects, the three species were scarcer in Morocco than in Spain. We did not find differences between the two countries in the number of power lines that are dangerous to raptors or in general impacts of agricultural intensification on bird populations (we assessed more farmland birds in Morocco). However, many more people (i.e., shepherds) were detected in Morocco, whose negative effect on raptors could explain the depletion of their populations. These transboundary differences are used to discuss the fate of these peripheral populations in a context of climate change and rural abandonment. They also highlight the need for strengthening raptor conservation around the Strait of Gibraltar, where a permanent flow of raptors converges throughout the year.