The amphicarpic annual Gymnarrhena micrantha (Asteraceae), inhabiting the deserts of North Africa to the Middle East, is interesting not only for its unusual biology, but also for its peculiar morphological structure. The monotypic genus Gymnarrhena, with uncertain position in the Asteraceae for a long time, is currently included in the tribe Gymnarrheneae and a separate subfamily Gymnarrhenoideae. The objective of the study was to examine fruit and seed structure in G. micrantha to consider possible phylogenetic relationships of the genus based on carpological characters. It was found that fruit structural organization in G. micrantha, with simply arranged pericarp and seed coat, parenchymatous and poorly differentiated on the tissue, corresponds to that of the early diverging evolutionary lines of Asteraceae, in which the states of these characters are considered to be plesiomorphic in the family. It has been suggested that taxonomically important structural features of Gymnarrhena cypsela include the structure of the apical region, pericarp and seed coat, the place of pappus attachment and its structure, the type of pappus hygroscopic tissue, and morphophysiological features of receptacular bracts surrounding the cypsela. The study did not confirm the relationship of Gymnarrhena with the tribes Corymbieae and Cichorieae, the seed coat of which differs markedly from the seed coat of Gymnarrhena in the presence of fine porosity of the exotesta cell walls. A set of the anatomical and carpological characters indicates a possible relationship of Gymnarrhena with the basal subtribes Cardopatiinae and Carlininae of the tribe Cardueae. The morphophysiological adaptation of G. micrantha and Cousiniopsis atractyloides cypselae to dissemination in desert conditions, similar in structural details, apparently suggests a close relationship between the subfamilies Gymnarrhenoideae and Carduoideae.