<p>Plants’ ecological responses to different edaphic conditions are important for understanding adaptation mechanisms. Its resilient physiology, unusual Ni hyperaccumulation pattern, and ability to thrive in extreme habitats such as serpentine and gypsum make <i>Odontarrhena sibirica</i> (Brassicaceae) an ecologically outstanding species. This study presents the first comparison of the ultrastructural adaptive differences in <i>Odontarrhena sibirica</i> individuals growing in serpentine and gypsum habitats using Scanning Electron Microscopy (SEM) analysis. Distinct habitat-related differences were observed in both vegetative and generative organs. Root tissues of specimens from serpentine habitats exhibited a more porous and heterogeneous organisation, whereas those from gypsum habitats appeared more compact and homogeneous. Differences were also observed in stem anatomy, including variations in epidermis thickness, cortex organisation, and xylem element structure, as well as wall thickening patterns. In leaves, the mesophyll was dominated by spongy parenchyma in specimens from both habitats. Tuberculate ornamentation of stellate trichomes was more pronounced in specimens from gypsum habitats. Floral surface structure also differed between habitats, with petal and style remnant surfaces of specimens from gypsum habitats showing more pronounced grooves and surface ornamentation. The observed ultrastructural differences may indicate that <i>Odontarrhena sibirica</i> exhibits substrate-related ultrastructural responses to selection pressures imposed by different edaphic conditions. Such patterns suggest that the species may display habitat-specific structural responses when growing under these challenging environments. This study offers valuable insights into plant adaptability under extreme edaphic conditions.</p>