The genus Ranunculus L., with a worldwide distribution, is the largest member of the Ranunculaceae. Here, nuclear ribosomal internal transcribed spacer (ITS) sequence data and chloroplast trnLF sequence data were used to analyze phylogenetic relationships among members of the annual and perennial (Group Praemorsa, Group Rhizomatosa, Group Grumosa and Group non-Grumosa) species of Ranunculus in Iran. In the strict consensus tree of nrDNA ITS sequence analyses, seven sub-clades were described, based on morphological, karyological, palynological, and ecological features. Within each clade, there were species belonging to more than one Group, and species of a single Group may fall into different clades, revealing that a classification based on underground system characters does not show natural interspecific relationships and must be revised. This is also apparent from trnL-F sequence analyses. Based on our results, the Praemorsa and Rhizomatosa Groups can be merged. The ITS sequence data show interspecific relationships more clearly than trnL-F sequence data. © 2011 Progress in Biological Sciences, Vol. 1, No.1, 41-47.