In the amphicarpic annual Gymnarrhena micrantha Desf. (Asteraceae), aerial and subterranean fruits differ in morphology, dispersal ability and germination behavior. The aim of our work was to study their structural features in relation to the eco-physiological properties, using light and scanning electron microscopes. Five fruit morphs were found, three of aerial achenes: ebracteate, bracteate and double bracteate ones, and two subterranean fruits with achenes, enveloped in involucral bracts, developed from (I) sessile or (II) not sessile different heads. This species shows divergent fruit differentiation, an increase in their diversity along several lines of morphological differentiation, which corresponds to a multiple seed dispersal and germination strategy. In addition to the already known distinctive features of subterranean achenes (larger size, undeveloped pappus, poor pubescence), they also differ in the simplified structure of the apical and basal achene regions, the absence of the corolla expanded base (cupula) and nectary, other cells parameters in the exotesta and endosperm, another form of the disproportionately developed embryo. The peculiarities of probably subterranean fruit II (seemingly originated through apomixis) extend to various color, pappus structure, sparse pubescence, and the ability of the fruit wall to delaminate. The lack of dense pubescence in the subterranean achenes is a key trait that could lead to increased water permeability of the fruit wall and affect germination rate. Possible adaptive significance of aerial achene structural features is discussed, including specialized corolla cupula, which may be an adaptation to dissemination by rainwater and ants.