Considering fundamental changes in the classification of angiosperms, based on phylogenetic studies, makes revising and updating Floras inevitable. Hence, in this paper, changes in the flora of Afghanistan have been listed and compared with the flora of Iran. As the latest studies indicate, according to APG IV system, the flora of Afghanistan comp-rises 40 orders, 130 families, about 1030 genera and 5065 species of angiosperms. In comparison the flora of Iran comprises 42 orders, 139 families, nearly 1252 genera and 8090 species of angiosperms. Moreover, the two countries share 39 orders, 124 families, 844 genera and about 1800 species. In Afghanistan the largest number of families belongs to Lamiales and in Iran to Caryophyllales. Asteraceae contains the largest number of genera in both countries. As far as the number of species in concerned, the largest angiosperms family in Afghanistan is Asteraceae, but in Iran it is Fabaceae. The most diverse ge-nera of both countries are Astragalus and Cousinia respectively. Gymnosperms have two orders, four families, seven genera and 22 species in Afghanistan, while in Iran they have two orders, three families, five genera and 17 species. By adding 58 species of pteridophytes and 311 species of bryophytes to Afghanistan’s flora and 60 species of pteridophytes and 534 spec-ies of bryophytes to Iran’s flora, in total, Embryophyta have approximately 5460 species in Afghanistan and 8700 species in Iran.