The aerial parts of Anthemis tinctoria L. and Angelica sylvestris L. and the roots of A. sylvestris have been used as traditional anticancer remedies in Estonian ethnomedicine. The aim of this study was to investigate content of essential oils (by gas chromatography) and polyphenolic compounds (using two different methods of high performance liquid chromatography–mass spectrometry (HPLC–MS)) of both plant species, as well as the in vitro anti-cancer effects of their essential oils and methanolic extracts. The average (n = 5 samples) yield of essential oils was 0.15%, 0.13%, and 0.17%, respectively. The principal compounds of the essential oil from the aerial parts of A. tinctoria were palmitic acid (15.3%), p-cymene (12.6%), and α-muurolene (12.5%), and α-pinene (45.4%), p-cymene (15.5%), and β-myrcene (13.3%) in aerial parts of A. sylvestris, while isocaryophyllene oxide (31.9%), α-bisabolol (17.5%), and α-pinene (12.4%) were the main constituents in the roots. The most abundant phenolic compounds in aerial parts were the derivatives of caffeic acid, quinic acid, and quercetin; the main compounds in roots of A. sylvestris were chlorogenic acid, quinic acid, and naringenin. The strongest anticancer effects were observed in essential oils of A. sylvestris roots and aerial parts on human carcinoma in the mouth cells (KB, IC50 19.73 μg/mL and 19.84 μg/mL, respectively). The essential oil of A. tinctoria showed a strong effect on KB and LNCaP cells (27.75–29.96 μg/mL). The methanolic extracts of both plants had no effect on the cancer cells studied.