The structure, diversity and dynamic of plant microbiota play a central role in plant productivity and plant health. There is increasing evidence that microbiota modulate defense and immunity mechanisms of plants, and vice versa. Thus, cooperative plant-microbe interactions can promote the recruitment of beneficial microorganisms and limit the development of pathogens. Our investigations are aimed at developing an innovative approach based on the characterization of the sugarcane microbiota during disease epidemic phases occurring in varietal selection processes. Our initial objective is to decipher the microbiota and virobiota diversity of a sugarcane variery infected by two pathogens: Xanthomonas albilineans (Xa) and sugarcane mosaic virus (SCMV) causing leaf scald and mosaic, respectively. Plants of cultivar CP16-1488 susceptible to the two diseases were inoculated with Xa, SCMV, or both pathogens in a replicated trial at Canal Point, FL in 2021. Several months after inoculation, leaf root, and stalk samples were collected from symptomless control plants and from plants exhibiting disease symptoms. Virobiota and microbiota diversity are currently analysed and preliminary data will be presented. Future investigations will include a larger number of sugarcane varieties and different collection sites to identify microbiota features of sugarcane pathobiomes. This project is expected to provide major insights into the role played by microbiota and virobiota in sugarcane plant health. It should lead to innovative precision farming and improvement of selection for stress-resistant sugarcane.