The present survey reports maximum parsimony (MP) and Bayesian phylogenetic analyses of the genus Potentilla L. in Iran using the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the trnL-F intergenic region of chloroplast DNA. A total of 25 taxa from 9 sections, 2 intersectional hybrids, and 4 related genera of Iranian taxa plus 40 previously sequenced data were analyzed for both trnL-F and nrDNA ITS regions. Individual and combined analysis of ITS and trnL/F data revealed monophyly of the genus Potentilla. The Potentilla core group was composed of monophyletic subclades of the sections Persicae (Th. Wolf) Juz., Potentilla, Micranthae Sojak., and Speciosae (Th. Wolf) Juz.; unresolved branches of the sections Rivales Poeverl., Aureae (Rydb.) Juz., Terminales,(Döll) Gren. & Godr., and Pensylvanicae Poeverl.; and the American genera Ivesia and Horkelia. The evolutionary trends of some diagnostic morphological traits were evaluated. Anther structure, and style shape and position evolved independently while multiple gains and parallel evolutions were inferred for leaf division.