Two new phenolic glycosides, 2,3-dihydroxybenzoic acid methyl ester 3-O-β-D-glucopyranosyl-(1-6)-β-D-glucopyranoside (1) and 2,5-dihydroxylbenzofuran 5-O-β-D-xylopyranosyl-(1-6)-O-β-D-glucopyranoside (2), were isolated as the minor chemical constituents from the roots of Gentiana rigescens, along with 15 known compounds. Their structures were elucidated by detailed spectroscopic analysis, including 1D, 2D NMR and chemical method. All of these compounds were isolated for the first time from the title plant. Moreover, compounds 1 and 2 were tested for the antifungal activities on three plant pathogens Peronophythora litchi, Glomerella cingulata, and Glorosprium musarum.