Flower morphology of ten Fritillaria species of subgenera Theresia and Fritillaria growing wild in Iran is studied using seventy morphological characters. Qualitative and quantitative datasets separated taxa into subgenera, sectional and groups. Three enigmatic species F. caucasica, F. zagrica (endemic to Zagros Mountains) and F. pinardii (recently reported from Zagros Mountains) appeared as closely related, distinct taxa. F. chlorantha (endemic to central Zagros Mountains) was put in an intermediate position between members of sections Trichostyleae and Olostyleae. Two distinct groups of taxa corresponding to Caucasian group and sect. Trichostyleae, were clustered in subgenus Fritillaria, mainly by three quantitative characters, i.e. lengths of petal, sepal, and the stamen. Exploratory analyses of both quantitative and qualitative characters produced consistent results and showed the application of quantitative characters of flower in refining the taxonomy of this genus.