The present study involves species A. monspessulanus L. and A. spruneri Boiss. section Incani DC. from the area of central Balkans. Due to high polymorphism, this section is taxonomically the most problematic group and delimitations of its species are not completely clear. The main aims of the study were to determine the micro-morphological and anatomical variability of populations of these species based on quantitative characters of leaflet and leaf petiole, and also to show the potential degree of differentiation within species. Additional goal was to determine anatomic parameters that may be used in taxonomy of studied species and their encompassing section. The results indicate high variability of analyzed characters and anatomical differentiation of populations of each species. Results of statistical analyses indicate that characters which refer to petiole anatomy have higher taxonomic value than characters which refer to leaflet anatomy. Anatomical features described in this paper mostly agree with characters found in previous studies of other Astragalus species, and they have potential taxonomic significance.