Thyme (Thymus spp.) is a valuable genus of Lamiaceae family presents a wide range of functional possibilities in the cosmetic, pharmacy, and food industries. T. daenensis and T. pubescens are thymol and carvacrol rich species growing in Iran. The aim of this study was to compare the macro- and micro-morphological, cytogenetical, and biochemical traits present in hermaphrodites and females of T. daenensis and T. pubescens. The analyses were performed by light microscopy (LM) to be compatible with scanning electron microscope (SEM) and gas chromatograph–mass spectrometry (GC–MS). The principal component analysis (PCA) loading plot was carried out using the original numerical data of quantitative characters (e.g., morphological, functional, and life-history traits). Results of gynodioecy analysis showed that the distribution of females in T. daenensis (58.33%) was significantly more than T. pubescens (9.1%). Peltate and capitate glandular trichomes (PGTs and CGTs, respectively) existed in both hermaphrodites and females of T. daenensis and T. pubescens. The size of PGTs in hermaphrodites was significantly larger than these GTs in females. The highest level of thymol and carvacrol was observed in both sexes of T. daenensis and T. pubescens, respectively. The results of the non-metric multidimensional scaling (NMDS) ordination showed separation of hermaphrodite and female types according to essential oil (EO) components. Based on the flow cytometric analysis, the obtained histograms confirmed that T. pubescens and T. daenensis were diploid and tetraploid, respectively. Variation among species and environmental/geographical factors result is differences in the content of thymol and carvacrol in various Thymus species which should be taken into consideration when applying these plants as therapeutic products.

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