The present study investigates the pollen morphology of 12 species belonging to the genera Ammannia, Lythrum, and Rotala of the family Lythraceae in Iran using light microscope and scanning electron microscope. The pollen grains are oblate, suboblate, oblate spheroidal, spheroidal, prolate spheroidal, subprolate and prolate, tricolporate with three or six alternating pseudocolpi (heteroaperturate), striate or rugulate exine sculpturing, microverrucate to microbaculate and microechinate colpus membrane, microverrucate to microbaculate, and psilate pseudocolpi membrane sculpturing types. The results revealed that these characters are taxonomically informative and can be used to identify the three studied genera and their species. We used multivariate analysis to understand the importance of pollen morphological data in determining genera and species relationships. Our findings revealed that the pollen qualitative traits have significant role in determining the generic delimitation.