Wild species are valuable resources for developing resilient crops to environmental stresses. We used Gossypium robinsonii, Australian wild cotton, to investigate the molecular signatures contributing to the tolerance of this plant to harsh environments. Three stages of pollen development, including tetrads (TE; 5-5.5mm), uninucleate microspores (UN; 7-10mm) and binucleate microspores (BN; 13-24mm) were exposed to 36/25 °C (moderate heat) or 40/30 °C (extreme heat) for 5 days, and the corresponding mature pollen grains were collected for SWATH-MS analysis. The genome of G. robinsonii assembled in the present study was used for proteome reference.