Astragalus (Fabaceae) includes many closely related species that are often difficult to distinguish. Within the section Poterion, A. bruguieri and A. baba-alliar subsp. nudicarpus are morphologically similar, and the latter has sometimes been treated as a variety of the former. This study aimed to clarify their taxonomic boundaries using morpho-anatomical evidence and identify reliable diagnostic traits. Forty-five populations were sampled from natural habitats in western and southwestern Iran. Plant specimens were identified using comprehensive floras and herbarium references. For morphometric analyses, at least ten mature individuals per site were measured with three replicates per organ. Transverse sections of stems and leaflets were prepared, double-stained with methylene blue and carmine alum, and examined under a light microscope; the epidermis was further stained with fuchsin. Data were analyzed using NTSYS software, with PCoA and the Mantel test. A. bruguieri grows as short shrubs (mean 50 cm), whereas subsp. nudicarpus reaches nearly three times this height and bears smaller stipules (1–2 mm vs. 5–6 mm). In A. bruguieri, leaflets are glabrous and ovaries pubescent, while traits are reversed in the subspecies. Their distribution patterns also differ: A. bruguieri occurs across several Middle Eastern countries at lower elevations on calcareous soils, whereas subsp. nudicarpus is restricted to Iran and prefers higher elevations with light soils, indicating distinct though overlapping phytogeographical regions. Anatomically, vascular bundles in stems are smaller in A. bruguieri (50–60 µm vs. up to 80 µm), and its leaflets have more lateral veins (4–5 vs. 2). In subsp. nudicarpus, epidermal cell number and stomatal density reach up to 250 cells and 20 stomata per mm², both considerably lower in A. bruguieri. This study highlights the importance of morpho-anatomical traits in distinguishing closely related Astragalus taxa. However, the taxonomic position of subsp. nudicarpus requires further investigation, including molecular phylogenetic analyses.