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To evaluate the effects of desert scrub habitat fragmentation on resident and migrant populations of Red-tailed Hawk and American Kestrel, we conducted monthly raptor road surveys during two years, 2008 and 2009, in natural desert scrub areas and in fragmented areas of Baja California Sur, México. We recorded 1,806 records of the two raptor species. The most common was the American Kestrel with 1,164 (64.4%) records (51% found in fragmented area, and 49% in natural area). The Redtailed Hawk accounted for 642 records (35.6%) (70% in fragmented areas, and 30% in natural areas). The relative abundance and density of Red-tailed Hawk in the spring and summer were similar between areas, but in the fall and winter the abundances and densities were much higher in fragmented areas. The abundance of American Kestrel was similar between areas in all seasons. Density was similar between areas in spring, summer and winter but it was higher in fragmented areas in the fall. The desert scrub of Baja California Sur and fragmented areas inside a cultivated agricultural matrix is an important habitat for migrant populations of both raptor species as indicated by the results of the fall and winter seasons. We discuss on the raptor species tolerance to habitat changes (threshold concept) as a function of their body size and habitat specialization (for nesting and foraging activities) and on the effects of fragmentation of desert scrub habitats on the abundance and density of the Red-tailed Hawk and American Kestrel in southern Baja California peninsula. [ABSTRACT FROM AUTHOR]