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The sensitivity of population trends to the climate and environment is generally considered a species-specific trait. However, evidence that populations may show different responses to the climate and environmental conditions is growing. Whether this differential sensitivity may arise even among neighboring populations remains elusive. We compared the trends of two neighboring populations of the Lesser Kestrel Falco naumanni, using data from a 12-year survey of 158 colonies in Sicily, Italy; the two populations inhabiting a lowland and an highland area, respectively. Population trends were modeled through the TRIM algorithms implemented in R (package rtrim). A reversed U-shaped population trend was observed in the lowland, while the highland population showed oscillations around a stable trend. Sahel rainfall 2 years before each annual survey significantly affected population variation in the lowland, while rainfall in March and an index of primary productivity in the breeding areas affected population variation in the highland. This suggests that the population in the lowland may be limited mainly by winter survival in Sahel, because the lowland may be an optimal breeding area for this species. In contrast, the highland population, which occupies a different part of the climatic niche of the species, may be limited mainly by reproductive output, because rainfall in March and the primary productivity in May could represent prey availability immediately before and during the breeding months. Overall, our findings suggest that population-specific environmental sensitivity might occur even over small (<100 km) geographical scales, highlighting the need for population-specific conservation strategies.