In this study, the anatomical and micromorphological structure, karyological characteristics and biochemical content of Scutellaria orientalis subsp. virens and endemic Scutellaria salviifolia, whose distributions areas overlap, were compared. Some anatomical and micromorphological differences were observed on the taxa; scleranchymatic pericycle layer on the stem, stomata density, distribution of trichomes, as well as the main vascular bundle and general shape of the petiole. The chromosome numbers of both taxa were determined as 2n = 22. However, there was a difference between chromosome length range and total chromosome length. The chromosome numbers and chromosome morphologies of these species have been defined for the first time in this paper. Differences in biochemical content were observed between species. Chlorophyll a (Chl a), total chlorophyll (Total Chl), total carbohydrate and malondialdehyde (MDA) contents were determined higher in leaf and stem samples of S. orientalis subsp. virens than S. salviifolia. There was no significant difference between the two taxa in terms of chlorophyll b (Chl b) content. Carotenoid (Car) content was detected higher in leaves samples of S. orientalis subsp. virens, but no significant difference was found between stems samples. Also, the effect of taxa on biochemical contents in relation to the habitat they live in is given in this study.