The aim of this work was to study the chemical composition, antioxidant and antibacterial properties of Achillea distans Waldst. et Kit. subsp. distans and Achillea distans Waldst. et Kit. subsp. alpina Rochel, from the Rodna Mountains (Romania). The identification and quantification of major phenolic compounds was performed by a HPLC-MS method. The total polyphenolic and flavonoid content was determined spectrophotometrically. The antioxidant activity was evaluated using the DPPH bleaching method, trolox equivalent antioxidant capacity assay (TEAC), hemoglobin ascorbate peroxidase activity inhibition (HAPX) assay, and an Electron Paramagnetic Resonance (EPR) spectroscopy method. A data indicated that A. distans subsp. alpina extract has more antioxidant activity than A. distans subsp. distans extract. Luteolin, apigenin, quercetin, caffeic and chlorogenic acids were present in the two extracts of A. distans, but in different amounts. Three flavonoids were detected only in A. distans subsp. alpina. The polyphenol-richer A. distans subsp. alpina extract showed a higher antioxidant activity than A. distans subsp. distans extract. A. distans subsp. distans extract showed inhibitory activity for Gram-positive bacteria, as evaluated with four species. The quantitative and qualitative differences between the two subspecies of Achillea distans could be used as a potential taxonomic marker in order to distinguish the species.