Aim Our aim was to understand the interplay of heterogeneous climatic and spatial landscapes in shaping the distribution of nuclear microsatellite variation in burrowing parrots, Cyanoliseus patagonus. Given the marked phenotypic dif ferences between populations of burrowing parrots we hypothesized an impor tant role of geographical as well climatic heterogeneity in the population structure of this species.Location Southern South America.Methods We applied a landscape genetics approach to investigate the explicit patterns of genetic spatial autocorrelation based on both geography and climate using spatial principal component analysis (sPCA). This necessitated a novel statistical estimation of the species climatic landscape, considering temperature and precipitation based variables separately to evaluate their weight in shaping the distribution of genetic variation in our model system.Results Geographical and climatic heterogeneity successfully explained molec ular variance in burrowing parrots. sPCA divided the species distribution into two main areas, Patagonia and the pre Andes, which were connected by an area of geographical and climatic transition. Moreover, sPCA revealed cryptic and conservation relevant genetic structure: the pre Andean populations and the transition localities were each divided into two groups, each management units for conservation.Main conclusions sPCA, a method originally developed for spatial genetics, allowed us to unravel the genetic structure related to spatial and climatic land scapes and to visualize these patterns in landscape space. These novel climatic inferences underscore the importance of our modified sPCA approach in revealing how climatic variables can drive cryptic patterns of genetic structure, making the approach potentially useful in the study of any species distributed over a climatically heterogeneous landscape.