We used 16S Illumina sequencing to define the leaf- and root-associated microbiomes of citrus trees across several variables, including Huanglongbing (Citrus greening) disease symptom severity, location, citrus cultivar, season, and time. This plant host/disease model was used to investigate: (a) the relationship between leaf- and root-associated microbial communities and host plant, (b) the interactions between native microbiota and a phytopathogen (i.e., Liberibacter, the causative agent of Huanglongbing), and (c) the core microbiota, their prevalence among broader microbial communities, and correlations between community structure and plant disease, among other factors.