A new species, Trigonella khalkhalica Ranjbar & Z. Hajmoradi (Fabaceae), endemic to Ardebil Province in northwestern Iran and belonging to Trigonella L. sect. Ellipticae (Boiss.) Širj., is described and illustrated. This species is mainly distinguished from T. elliptica Boiss. of Trigonella sect. Ellipticae by some differences such as plant height (41–65 cm vs. 30–40[50] cm), indumentum (sparse to glabrous vs. dense), and fruit shape (lunate vs. erect). Trigonella elliptica is selected for comparison with the new species because it is similar to T. khalkhalica in fruit characters (the size of pods, sculpturing, and number of seeds) and has a widespread distribution in Iran. The remaining taxa in the section have more restricted distributions. Morphological and anatomical studies on vegetative and floral structures (including pollen, peduncle, stem, and leaf epidermis) are discussed for both species. Variation in some noticeable pollen and anatomical features were observed in the two species. The most significant pollen characters for separating the new species from T. elliptica are the polar and equatorial diameters, the colpus interval, and pollen shape. Differential anatomical characters include the stem shape in cross-section and number of sclerenchyma layers, the number of vascular bundles in the stem and peduncle, and also the size and index of stomata in the leaf epidermis.