Abstract Tea ( Camellia sinensis (L.) O. Kuntze) is a commercially important crop valued for its secondary metabolites. Different cultivation methods affect tea quality by altering the biosynthesis of flavonoids. Shade can effectively improve the quality of tea beverages by causing reduction of the concentration of flavonoids, the main compounds that contribute to astringency, in the leaves. The aim of this study was to analyze the influence of shade on flavonoid biosynthesis in relation to expression of the flavonoid pathway genes in tea leaves. Our data revealed that shade had notable effects on both flavonoid (including catechins, O -glycosylated flavonols and proanthocyanins (PAs)) and lignin biosynthesis, but had no significant effect on anthocyanin accumulation. Among all the detected compounds, the concentration of PAs and O -glycosylated flavonols in shaded leaves changed more than other compounds, decreasing 53.37% and 43.26%, respectively, compared to the sunlight-exposed leaves. Expression of phenylalanine ammonialyase ( PAL ), flavanone 3-hydroxylase ( F3H ), flavonoid 3′-hydroxylase ( F3 ′ H ), dihydroflavonol reductase ( DFR ) and anthocyanidin reductase1 ( ANR1 ) was notably correlated with the concentration of PAs in leaves, and expression of chalcone synthase ( CHS ) and flavonoid 3′,5′-hydroxylase ( F3 ′ 5 ′ H ) was remarkably correlated with the concentration of O -glycosylated flavonols. It is suggested that polymerization of catechins and glycosylation of flavonols might be key pathways of flavonoid metabolism in tea leaves affected by shade treatment. Regarding phenolic acids, a marked increase in concentration in shaded leaves and negative correlation with lignin accumulation suggests that phenolic acids might compete for the same substrate with lignins and flavonoids in tea leaves under different illumination conditions. Further investigations are required to understand the relationship between phenolic acids and other flavonoid compounds in tea plants.