Astragalus L. sect. Aegacantha Bunge includes 57 described species, mostly confined to Southwest Asia and Central Asia. We studied the pollen morphology of 17 species of this section present in Pakistan. Pollen morphology of sect. Aegacantha species is poorly investigated despite its systematic importance. The main aim of this study is to determine and document the pollen characters that can assist in the taxonomic identification of species in this difficult section. Pollen slides were prepared following acetolysis and examined by both light and scanning electron microscopy. Pollen size varies, with the polar axis ranging from 32.91 to 43.10 µm and the equatorial axis from 22.91 to 28.47 µm. Pollen is sub-prolate (1.15–1.33) to prolate (1.34–2.00) in shape, small to medium in size, radially symmetrical, isopolar, trizonocolporate to tricolporate, and monad. Sculpture variations (i.e. reticulate, microreticulate, perforate, microperforate, regulate, microregulate and granulate) were observed around the apertural, meridional and polar regions. Ordination analysis (principal component analysis (PCA)) revealed that the quantitative characters of pollen morphology are the most reliable characters for delimitation of species within section Aegacantha. Cluster analysis (unweighted pair group method using arithmetic average (UPGMA)) shows a partial relationship between the Aegacantha taxa clustered based on pollen characters and supports the general morphology. Further, this study shows that the pollen traits provide a baseline for phylogenetic optimisation in the investigated Aegacantha section.