East Coast Fever (ECF) is a livestock disease caused by Theileria parva, a protozoan transmitted by the vector tick Rhipicephalus appendiculatus. This disease causes high mortality in cattle populations of Central and Eastern Africa, especially in exotic breeds. Here, we highlight genomic regions likely involved into tolerance/resistance mechanisms against ECF, and we introduce the estimation of their Spatial Area of Genotype Probability (SPAG) to delimit areas where the concerned genotypes are predicted to be present. During the NEXTGEN project, 803 Ugandan cattle were geo-referenced and genotyped (54K SNPs), while 532 tick occurrences were retrieved from a published database. To get a proxy of the parasite selective pressure, we used WorldClim bioclimatic variables to model vector ecological niche. Landscape genomics models were then used to detect cattle genotypes associated with vector probability of presence, and to estimate their SPAGs. Finally, climate change scenarios for 2070 were considered to compare the predicted shift in the vector niche with the estimated current SPAG. The analysis revealed two main areas of presence of possibly resistance-related genotypes, one South and one East of Lake Victoria. Climate change will probably shift tick niche southwards in the Eastern regions of Lake Victoria, inducing a critical area that currently does not show the candidate genotypes, but where disease will likely spread in the future. The combined use of SPAGs and niche maps could therefore facilitate the identification of regions of concern and to direct future targeted breeding schemes.