The present study investigates the morpho-anatomical variations of cypselae in three species of the tribe Madieae (Asteraceae), namely Arnica acaulis (Walter) Britton, Sterns & Poggenb., Arnica unalaschcensis Less., and Eriophyllum lanatum (Pursh) J. Forbes. Detailed external and internal characteristics of cypselae were examined using both light microscopy and scanning electron microscopy. Morphologically, parameters such as cypsela shape and size, color, pappus structure, stylopodia morphology, surface features, and the presence or absence of hairs were analyzed. In all species studied, the upper portion of the cypsela bears a persistent pappus, which consists of multicellular, terete bristles in Arnica acaulis and Arnica unalaschcensis (barbellate), or scaly, large, and paleaceous bristles in Eriophyllum lanatum. The presence of a carpophodium was also noted across all species. Anatomically, the cellular structure of the pericarpic region was scrutinized, revealing that in Arnica unalaschcensis and Eriophyllum lanatum, the pericarp is thick and differentiated into an epicarp and mesocarp. Additionally, a non-cellular, black, carbonized resinous layer, identified as a phytomelanin layer, was consistently observed beneath the epicarp and above the sclerenchymatous zone in all species. An artificial key for the studied species has been provided to facilitate their identification. The findings of this study hold significant taxonomic implications, offering a reliable basis for the identification of these taxa.