Resistance (R) genes are directly or indirectly involved in the activation of the plant immune systems. Despite their essential roles in defense against a variety of pathogens, very little is known about their classification as well as associated decoy domains, particularly in crop plants. Using advanced bioinformatics strategies, this study provided a complete classification of all R genes in three cotton species, G. arboreum (Ga), G. raimondii (Gr) and G. hirsutum (Gh)). A total of 3085, 3024 and 5355 R genes were identified in Ga, Gr and Gh, respectively and these were classified into fifteen major classes based on R domains. Moreover, we identified several decoy domains associated with the R domains mainly comprising DUF, Lectin_legB, WRKY and Calmodulin_binding domains. Interestingly, most of the identified decoy domains belong to stress-responsive protein families. Furthermore, the comparison among the cotton genomes suggested the gain and loss of R gene classes displaying the evolutionary divergence of these three genomes. Finally, promoter analysis also predicted different cis-acting sites in different NBS-containing R gene classes. Overall this study provides in-depth genome-wide insights into R genes and their associated decoy domains in cotton, and potentially also appears as a reference study on R genes for other agronomically important crops.