Coffee represents the most important non-alcoholic beverage in world trade and its cultivation has a significant socioeconomic impact on the development of the populations involved in multiple regions of the world, including those directly affected by climate change. Thus, the increase in temperature and changes in the behaviour of rainfall have given rise to epidemics of microbial diseases such as orange rust caused by the fungus Hemileia vastratix. Coffee growers and authorities in various countries have sought control alternatives such as conventional genetic improvement, biological control, and recently the generation of resistant varieties by inducing mutations. However, many of them have not given the desired results in part because the genetic, ecological and functional interactions of this fungal pathogen with the microbial community of the coffee phyllosphere and the possible effect of the latter on the control of the disease are still unknown. Some initial studies have been carried out in Brazil, Colombia and Mexico, but none in Costa Rica, which is relevant because the endophytic communities change significantly from one geographical area to another. Likewise, studies on endophytic communities in other Rubiaceae plants are very scarce, especially for bacteria. Most studies on Rubiaceae endophytic bacteria deal with nodule-dwelling bacteria, but few have characterized the entire microbiome (bacteria + fungi). This research proposal aims to identify and characterize the microbiome in the phylosphere of commercial varieties and mutant coffee plants (Coffea arabica L.) generated in previous research projects in order to determine the interaction of endosymbiotic microorganisms and the effect on the metabolome, plant physiology and symptom expression of the disease caused by the orange rust fungus (Hemileia vastatrix). For this purpose, in the first instance, the bacterial and fungal community associated with orange rust will be identified in the phyllosphere of mutant plants and commercial varieties of coffee. Once identified, in a second stage, we propose to analyse the effect of the exogenous application of previously identified bacteria and fungi, as well as drought and temperature on the microbiome associated with orange rust. This will be possible thanks to the consolidation of a research group made up of experts in plant biotechnology, genetic improvement, microbial ecology and bacterial genomics, mycology, allowing the extension of previous research carried out in the area of genetic improvement of coffee. The anticipated results will allow expanding and deepening the knowledge generated by the research group and will serve to compare how the microbiome changes in the presence of rust and in different genotypes of coffee plants. The addition of the characterization of endophytic bacteria and fungi will lead to a better understanding of the interactions of a microbiome (bacteria + fungi) and their contribution to the health of coffee plants.