The current range of European vipers is mostly parapatric but local-scale allopatric distribution is common and few cases of sympatry are known. In the High Course of Ebro River, northern Spain, there is a contact zone between Vipera aspis, V. latastei, and V. seoanei. Sympatry was detected between aspis and latastei and also specimens with intermediate morphological traits. Presence-data at a local scale (1 × 1 km) and ecological niche-based models manipulated in a GIS were used to (1) identify how environmental factors correlate with the distribution of the three vipers and with the location of the sympatry area, and (2) identify potential areas for viper occurrence and sympatry. Ensemble for casting with 10 Maximum Entropy models identified a mixture of topographical (altitude, slope), climatic (precipitation, evapotranspiration, and minimum and maximum temperature), and habitat factors (land cover) as predictors for viper occurrence. Similar predicted probabilities according to the variation of some environmental factors (indicating probable sympatry) were observed only for aspis-latastei and aspis-seoanei. In fact, areas of probable occurrence of vipers were generally allopatric but probable sympatry between vipers was identified for aspis-latastei in 76 UTM 1 × 1 km squares, for aspis-seoanei in 23 squares, and latastei-seoanei in two squares. Environmental factors correlate with the location of this contact zone by shaping the species range: some enhance spatial exclusion and constrain distribution to spatially non-overlapping ranges, while others allow contact between species. The distribution in the contact zone apparently results from the balance between the pressures exerted by the different environmental factors and in the sympatry area probably by interspecific competition. Further ecological and genetical data are needed to evaluate the dynamics of the probable hybrid zone. GIS and niche-modelling tools proved to be powerful tools to identify environmental factors sustaining the location of contact zones.