The genus Lallemantia Fisch. & C. A. Mey. (Family Lamiaceae) is a small genus with only five species that are herbaceous annual or biennial plants with food and medicinal value. This genus is of Caucasian origin and contains 5 species in Iran. The aims of the present study were: 1-to examine the occurrence of phylogenetic conflict between nuclear (ribosome ITS), nuclear repetitive sequences (ISSRs) and plastid (rps16 intron, cp) sequences in the genus Lallemantia (Lamiaceae), 2-to investigate the occurrence of inter-specific hybridization in this genus, and 3-to compare the time of divergence of the species from the basal line by ITS and cp-DNA molecular data. This is the first analysis on these evolutionary aspects of the genus Lallemantia. We provided the first molecular evidence for the occurrence of inter-specific hybridization in the genus Lallemantia and illustrated that phylogenetic signals in cp-DNA and ITS sequences differ significantly.