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Proline-rich extensin-like receptor kinases (<i>PERKs</i>) are an important class of receptor kinases in plants. Receptor kinases comprise large gene families in many plant species, including the 15 <i>PERK</i> genes in <i>Arabidopsis</i>. At present, there is no comprehensive published study of <i>PERK</i> genes in <i>G. hirsutum</i>. Our study identified 33 <i>PERK</i> genes in <i>G. hirsutum</i>. Phylogenetic analysis of conserved PERK protein sequences from 15 plant species grouped them into four well defined clades. The <i>GhPERK</i> gene family is an evolutionarily advanced gene family that lost its introns over time. Several <i>cis</i>-elements were identified in the promoter regions of the <i>GhPERK</i> genes that are important in regulating growth, development, light responses and the response to several stresses. In addition, we found evidence for gene loss or addition through segmental or whole genome duplication in cotton. Gene duplication and synteny analysis identified 149 orthologous/paralogous gene pairs. Ka/Ks values show that most <i>GhPERK</i> genes experienced strong purifying selection during the rapid evolution of the gene family. <i>GhPERK</i> genes showed high expression levels in leaves and during ovule development. Furthermore, the expression of <i>GhPERK</i> genes can be regulated by abiotic stresses and phytohormone treatments. Additionally, <i>PERK</i> genes could be involved in several molecular, biological and physiological processes that might be the result of functional divergence.