<p>Purple acid phosphatase (PAP) genes are central to plant phosphorus metabolism and stress adaptation. However, their genome-wide characterization and functional roles in cotton remain unclear. Cotton often faces phosphorus limitation, affecting growth and fiber yield. In this study, we performed a comprehensive genome-wide analysis of <i>PAP</i> genes in four cotton species to elucidate their evolutionary patterns and potential roles in phosphorus use efficiency, stress response, and fiber development. A total of 202 PAP encoded proteins were identified, with 63 in <i>G. hirsutum</i>, 69 in <i>G. barbadense</i>, 35 each in <i>G. arboreum</i>, and <i>G. raimondii</i>, which were classified into eight conserved subgroups. Gene structure, motif composition, and phylogenetic analysis revealed strong evolutionary conservation with evidence of subfunctionalization. Chromosomal mapping, collinearity, and Ka/Ks analysis indicated that segmental and whole-genome duplications primarily drove <i>PAP</i> expansion, with most genes retained under purifying selection. Promoter analysis uncovered abundant cis-elements associated with stress and hormone responses, suggesting tight transcriptional regulation under developmental and experimental cues. Expression profiling revealed tissue-specific and Pi-responsive regulation, highlighting the involvement of PAPs in root Pi acquisition, reproductive growth, and fiber development. Co-expression analysis further identified key hub genes, regulating vegetative growth (<i>Gh_A13G1171</i>), reproduction (<i>Gh_D05G1806</i>), fiber development (<i>Gh_D05G0522</i>), and P metabolism (<i>Gh_A03G0451</i>). Collectively, this study provides the first systematic characterization of the cotton PAP gene family, offering new insights into their evolutionary dynamics and functional roles, and identifies promising genetic targets for improving P use efficiency and stress resilience in cotton.</p>