In plants, the developmental transition from a dark condition to the light results in the activation or repression of multiple developmental response elements affecting plant photomorphogenesis. In this developmental switch one of key positive regulators of photomorphogenesis is the bZIP transcription factor HY5. Mutation in this gene in Arabidopsis causes abnormal elongation of hypocotyl and root hairs in the light. We hypothesize that HY5 or a HY5 paralog could play a role in the regulation of cotton fiber elongation by the phytochrome genes, in particular PHYB. Recent initial findings about the possible influence of red and far-red light on cotton fiber development serve to justify the investigation of light-dependent genes of cotton in order to further understand the molecular basis of cotton fiber elongation at the developmental level. Therefore, we have cloned and characterized orthologs of the Arabidopsis HY5 gene from Gossypium species. We found that tetraploid cottons G. hirsutum and G. barbadense have at least two orthologous genes for HY5 that were acquired from the putative diploid ancestors – G. raimondii (D-genome) and G. herbaceum (A-genome) — through allopolyploidization. The expression level of cotton HY5 genes in light grown and dark-grown seedlings of Upland cotton (G. hirsutum) was determined. The biological function of Gossypium-derived cotton HY5 loci is being studied through RNA interference to reveal involvement of HY5 genes in fiber development process. 'Candidate gene' markers have been developed to tag important QTLs associated with HY5 function in cotton. The evolutionary relatedness of cotton and Arabidopsis HY5 will be discussed.