Abstract: Using high performance liquid chromatography (HPLC) and microplate spectrophotometer, we determined variations in pigments and enzymes phenylalanine ammonialyase (PAL) and UDP glucose-flavonoid 3-O-glucosyl-transferase (UFGT) involved in biosynthesis pathway of anthocyanins in Sabina przewalskii and Picea crassifolia along with altitude changes. The content of pigments and enzyme activity were dependent on the altitude: the anthocyanins (Acy) increased between 3 100–3 200 m, decreased with the increase of altitude in general. The enzyme activity of UFGT was increased with the increase of altitude while it fluctuated around 3 000 m. The enzyme activity of PAL in S. przewalskii was increased with the increase of altitude and the same pattern appeared in P. crassifolia between 2 800–3 000 m. The enzyme activity of PAL in P. crassifolia was decreased with the increase of altitude above 3 000 m. Contents of rhodoxanthin (Rhd) and carotenoids (Car), de-epoxidation index (A+Z)/(V+A+Z) were higher with higher altitude. The content of chlorophyll (Chl) had an opposite pattern: decreased with increasing altitude. Except for chlorophyll and PAL, the needles of S. przewalskii contained higher pigments than those of P. crassifolia. It was noted that the level of UFGT activity in S. przewalskii was twice that in P. crassifolia. Plants would encounter various environmental stresses caused by different altitude and season. Drought and strong sunlight are dominant in August for two species of Qilian Mountain. These pigments are mainly for anti-drought and prevent strong sunlight. Therefore, the role of pigments depends on when and where these plants inhabit.