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Lagochilus is a genus with ten taxa (species, subspecies and variety) in Iran, which nine of them are endemic. This is the first micromorphological investigation of this genus. Micromorphological features of trichomes on the stems, leaves and calyces, and also pollen morphology of 19 populations were investigated by scanning electron microscopy. Two types of trichome (glandular and non-glandular) including 14 forms were described. Here, among the non-glandular trichomes, cell number and size of trichomes are considered as valuable characteristics, while the glandular trichomes are observed as stalked, sessile and peltate. Lagochilus pollen grains are tricolpate and small to medium sized. The basic shape of the pollen grains in most taxa is prolate, however prolate-subprolate pollen grains was recorded for L. aucheri ssp. aucheri var. aucheri 2. Four types of exine sculpture patterns were distinguished: bireticulate, reticulate, microreticulate and incomplete reticulate. Quantitative and qualitative characteristics were examined by multivariate analysis. The results indicated that the studied taxa were separated from each other; however varieties of L. aucheri did not grouped together. The results support the existence of known varieties in L. aucheri. In general, our investigations reveal the usefulness of micromorphological characteristics in taxon delimitation at the specific and infraspecific levels.