Morphological characters of 10 species of Chara from different localities in northern, western and central Iran have been analyzed, with Nitella hyalina and Tolypella glomerata as outgroups. Phenetic and cladistics analyses of populations belonging to the 10 Chara species were undertaken to reveal their inter‐population morphological variation and inter‐specific relationships. Clustering was based on 54 characters (41 qualitative and 13 quantitative). This produced two major clusters, grouping Chara crassicauliss, C. vulgaris var. longibracteata, C. vulgaris var. vulgaris and C. contraria separate from C. grovesii, C. gymnophylla var. gymnophylla, C. gymnophylla var. rohlenae, C. kirghisorum and C. tomentosa. A smaller cluster of C. socotrensioides, C. fibrosa and Chara sp. was separate from these two clusters. A factor analysis identified the most variable morphological characters as type of cortification, prescence and length of the spine cells, stipulode length, type of branchlet cortication, bract cells length, placement of the gametangia, character of end segment, length of branchlet and internode, development of posterior bract cells, oogonia length and width, oospore length, width and length/width ratio, fossa breath, and number of striae.