Climate change is negatively affecting the coffee value chain, with a direct effect on approximately 100 million people from 80 countries. This has been attributed to the high vulnerability of the two-mainstream species, Coffea arabica and Coffea canephora, to extreme weather events, with notable uneven increases in market prices. Taking into account the narrow genetic plasticity of the commercial coffee cultivars, wild-relatives and underutilized Coffea species are valuable genetic resources. In this work, we have assessed the occurrence of Coffea species in to understand the degree of genetic relationships between Coffea species in the country, as well as the patterns of genetic diversity, differentiation, and genetic structure. Only one wild species was found, C. racemosa, which showed a high level of genetic separation with C. arabica, based on plastid, as well as SSR and SNP analysis. C. arabica presented low levels of diversity likely related to their autogamous nature, while the allogamous C. racemosa presented higher levels of diversity and heterozygosity. The analysis of the functional pathways based on SNPs suggests that the stress signaling pathways are more robust in this species. This novel approach shows that it is vital to introduce more resilient species and increase genomic diversity in climate-smart practices.