Background: Citriculture holds significant socioeconomic importance but is adversely affected by diseases that reduce productivity. Plant disease resistance is typically relies on efficient defense mechanisms - PTI and ETI - involving PRR receptors and R genes responsible for pathogen recognition and the initiation of defense responses. Results: In silico analyses performed on 11 genomes of 10 Citrus species, as well one genome of each Poncirus trifoliata and Fortunella hindsii, enabled the identification and classification of PRR receptors and R genes, analysis of gene duplication and clusters, validation of findings using RNA-seq libraries, and assessment of inter- and intraspecific variability across 43 additional accessions. Conclusions: Our results show that PRR receptors and genes are organized in clusters and exhibit both inter- and intraspecific diversity, with wild citrus species presenting lower gene counts compared to ancestral and hybrid species. Wild species showed a predominance of membrane-associated PRRs (RLKs and RLPs), potentially linked to early pathogen recognition, whereas ancestral and hybrid species exhibited higher abundance of intracellular receptors (CNL and TNL). These patterns suggest distinct immune strategies among citrus species, although further functional studies are required to confirm their roles in PTI or ETI responses.