Historical and ecological processes have deeply affected biogeographic patterns of animals. Studying morphological variability of species, using classical and spatial analyses, can elucidate these patterns and give insights on both processes. Morphological variability of the endemic Iberian viper Vipera seoanei is examined to identify morphological coherent groups, biogeographic patterns and the putative role of abiotic pressures in the geographic variation of morphological variation. Results from classic and spatial multivariate analyses over 27 morphometric traits for 468 specimens from the global range of the species were integrated. Classic analyses reported large morphological variability and confirmed the differentiation of two coherent groups, which are representatives of current subspecies. Spatial analyses reported a geographic gradient pattern from western Cantabrian Mountains to the rest of the study area. Areas of high morphological variability were found, and two spatial coherent groups with an integration zone were recognized. Significant spatial correlations and trends suggest that some traits could be under selection and may display adaptations to local environments. Although observed patterns can be attributed to Pleistocene climatic cycles, an adaptive diversification of the species is supported. The combination of classical and spatial multivariate analyses is a useful methodology to identify morphological patterns and infer underlying factors.