Background <p>Drought stress is a significant global challenge that negatively impacts cotton fiber yield and quality. Although many drought-stress responsive genes have been identified in cotton species (<i>Gossypium</i> spp.), the diversity of drought response mechanisms across cotton species remains largely unexplored. This study compared gene expression modulation in response to drought stress across three diploid cotton species: <i>G. arboreum</i>, <i>G. stocksii</i>, and <i>G. bickii</i>.</p> Results <p>We observed significant variation in the content and biological roles of differentially expressed genes among the studied species, along with enhanced divergence in ortholog expression patterns under drought stress. These findings suggest a remodeling of drought response mechanisms during the independent evolution of cotton species. Additionally, we identified 287 genes exhibiting similar regulatory responses to drought across species, highlighting pathways including starch and sucrose metabolism, chlorophyll catabolite degradation and synthesis, and hormone-mediated signal transduction. Notably, 16 transcription factors were identified as potential central regulators of the conserved stress response mechanisms.</p> Conclusions <p>This study reveals the diversity of drought response mechanisms among individual cotton species, identifies valuable targets for genetically enhancing drought tolerance, and provides a strategic framework for identifying candidate genes for breeding programs.</p>