The family Lythraceae, belonging to the order Myrtales, comprises approximately 28 genera and 700 species of trees, shrubs, and herbs distributed in various regions of the world, especially in tropical and temperate regions. A phylogenetic study based on cpDNA trnH-psbA, nrDNA ITS, and combined sequences datasets were evaluated using maximum parsimony, Bayesian, and maximum likelihood methods. Most of the reconstructed trees revealed the monophyly of the three genera Lythrum, Ammannia, and Rotala in Iran. All trees supported the distinctiveness of species within these three genera. Additionally, the phylogenetic trees of the present study demonstrated the early divergence of Lythrum species on the lower branches and the derivation of Ammannia species on the higher clades and Rotala species on the terminal clades. The results of the phylogenetic study revealed the close relationship of some Lythrumspecies (such as L. thesioides M. Bieb. with L. silenoides Boiss. & Noë and three species L. thymifolia L., L. junceum Banks & Sol., and L. hyssopifolia L.) and Ammannia (A. coccinea Rottb. with A. multiflora Roxb., and A. baccifera L. with A. auriculata Willd.), indicating the need for taxonomic revision.