Aim: To compare the bioactivity of both polar and non-polar fraction of Origanum vulgare spp. hirtum methanolic extract on Chlamydomonas reinhardtii. Material and methods: The polar and non-polar fractions were derived from aerial parts of Origanum vulgare ssp. hirtum, collected during the flowering stage from the ex-situ collection of IBER-BAS. GC/MS analysis of both fractions was done following the standard protocol. The measured mass spectra were deconvoluted by the Automated Mass Spectral Deconvolution and Identification System (AMDIS), before comparison with the databases. Chlamydomonas reinhardtii 137C+ (WT) was used as a test system. Spot-test, cell survival fraction (SF), test of “visible mutations” and CFGE (for measurement of induced DNA double-strand breaks (DSBs)) were applied. Results: The polar fraction did not possess genotoxic, mutagenic as well as DNA-damaging effect. The situation with the non-polar fraction was quite different. Even at the lowest concentration of 250 ppm, cell survival was decreased by 60% (SF = 0.41 ± 0.08). Treatment with concentrations equal to/or greater than 500 ppm resulted in around 100% lethality. A mild mutagenic effect was obtained for the concentration of 250 ppm non-polar fraction (IM = 4.83 ± 0.004). Well-expressed and concentration-dependent induction of DSBs for even the strong DNA fragmentation was observed after the treatment with the non-polar fraction. Conclusions: The different bioactivity of the two fractions correlated well with their different chemical composition. The polar fraction, rich in sugars, organic acids and flavonoid glycosides, did not possess genotoxic and mutagenic potential. The strong genotoxic potential of the non-polar fraction might be related to carvacrol content (37.08%), which is not present in the composition of the polar fraction. To the best of our knowledge, this study provides the first information that the carvacrol-rich non-polar fraction of Origanum vulgare spp. hirtum methanolic extract possesses genotoxic, mutagenic and DNA damaging effect on some low eukaryotes, such as C. reinhardtii. Further experiments with carvacrol should be done in order to clarify the exact mechanism of action.