Phytochromes are known to play roles in cotton plant architecture, floral initiation, and fiber elongation. Previously in our laboratory, we characterized the Gossypium orthologs of the Arabidopsis PHYA, PHYB, PHYE and HY5 genes from G. hirsutum and G. barbadense (AD-genomes), and from G. herbaceum (A-genome) and G. raimondii (D-genome). Based on SNP sites in Gossypium-derived PHY genes, several phytochrome-specific CAPs and dCAPs markers were developed for PHYA1, PHYB1, PHYB2 and HY5 genes to reveal their association with important QTLs in interspecific populations of G. hirsutum and G. barbadense. Using these ‘candidate-gene’ markers, cotton phytochrome genes were assigned in specific cotton chromosomes using cytogenetic stocks of cotton, and incorporated into the genetic linkage map of cotton derived from the interspecific cross of TM1 (G. hirsutum) and 3-79 (G. barbadense).  Results of both analyses with cytogenetic stocks and linkage mapping revealed that PHYA genes located in chromosome 11, PHYB genes are in chromosome 10 and HY5 gene is chromosome 24. The association of these phytochrome-specific ‘candidate’ gene markers with useful agronomic traits of cotton will be presented.