The aim of this article is to study the relationship between biosynthesis of anthocyanin and activities of phenylalanine ammonia lyase (PAL), chalcone ismoerase (CHI) enzymes in Pyrus pyrifolia. Changes in the level of anthocyanin and the activities of enzymes of anthocyanin biosynthesis including PAL, CH1 were studied in the pericarp of Pyrus pyrifolia Aoguan and Mantianhong during the period of pigment formation. Bagging treatment was also carried out to manipulate the synthesis of anthocyanin and the activities of related enzymes during the period of pigment formation. The results demonstrated that the level of anthocyanin of Aoguan was higher than that of Mantianhong. However, the content of anthocyanins has the similar changing trend in Aoguan and Mantianhong, highest anthocyanin concentrations of two varieties appeared in immature fruit and faded toward harvest. Meanwhile, similar changing trends of activities of PAL and CHI were also observed in both varieties. Aoguan has a lower activity of PAL than Mantianhong, whereas activity of CHI in Aoguan was higher than that in Mantianhong. Activity of PAL decreased during the period of pigment formation and was apparently not limiting to color development, whereas CHI activity increased at the same period and was closely related to the synthesis of anthocyanin. The results of bagging treatment showed that bagging treatment inhibited the activity of CHI, as well as the synthesis of anthocyanin, whereas debagging enhanced both the activity of CHI and synthesis of anthocyanin. The activity of CHI in debagging Aoguan pericarp was higher than the untreated Aoguan. However, effect of bagging treatment toward PAL activity was not obvious. Anthocyanin of bagging treated Aoguan decreased toward harvest. The content of anthocyanin of Pyrus pyrifolia increased at the beginning of fruit coloration period and decreased toward fruit harvest. Activity of PAL was apparently not limiting to color development, whereas CHI activity was closely related to the synthesis of anthocyanin. Debagging enhanced both the activity of CHI and anthocyanin synthesis. Bagging treatment also proved that degradation of anthocyanin was not induced only by light. Light appeared to have two opposing effects in pears: it is required for anthocyanin synthesis and also for apparently increasing red color loss through increased degradation of anthocyanin.