We investigated leaves of Sabina przewalskii and Sabina chinensis for seasonal variations in the contents of anthocyanins (ANT), flavonoids (FLA), rhodoxanthins (RHO), chlorophylls (CHL) and carotenoids (CAR), as well as the activity of phenylalanine ammonialyase (PAL) and UDP glucose flavonoid glycosyltransferase (UFGT), the key synthetases of anthocyanins. The content of ANT and activities of PAL and UFGT were significantly higher in low-temperature months and were associated with changes in FLA, RHO and CAR of the two species. The variations in CHL were the opposite. The contents of ANT, FLA, RHO, CAR and CHL and activity of PAL and UFGT in S. przewalskii were higher than those in S. chinensis. The results suggested that ANT is an important secondary metabolite that has antifreezing properties and is an important protective substance that could resist low temperature and radiation stress. RHO and other pigments play an important role in resisting cold-induced photoinhibition.