Tick-borne diseases and especially protozoa of the genus Babesia, are gaining increasing attention as emerging zoonotic pathogens. Zoonotic species like B. venatorum and B. microti have wild animals as main reservoir hosts. We propose a habitat suitability model for Babesia spp., as tool for institutions and policy makes to better understand the entity of Babesia presence, to improve diagnostic awareness and to optimize screening and preventive actions. The probability of presence of Babesia spp. was estimated using as presence data, wild ruminants positive by PCR to Babesia spp. which were correlated to environmental factors that can favor or limit vector and host availability. We developed three separate models to discriminate the different roles of Red deer and Roe deer and Alpine chamois in Babesia spp. epidemiology. A comprehensive model using all presence data from all ungulates species was also developed. The overall suitable area for Babesia spp. in this simulation is of 3723 km2, which correspond to 15.51% of the background regional territory. The model developed was empirically validated assessing tick abundance in randomly chosen areas classified by the model as moderately or highly suitable for Babesia spp. Collected ticks were tested by PCR for Babesia spp. to confirm model predictions as infection prevalence with Babesia spp. was significantly higher in areas predicted as highly suitable compared to those classified by the model as moderately suitable for Babesia spp. (X2=5.05 p<0.05, Odds Ratio OR= 2.12 CI95% 1.1-4.1).