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In this preliminary study, the acidic hydrolysate fingerprints of polysaccharides based on hydrophilic-interaction chromatography-evaporative light scattering detection-electrospray time-of-flight mass spectrometry (HILIC-ELSD/ESI-TOF/MS) combined with multivariate statistical analysis was developed and applied to investigate the quality of Ganoderma lucidum from different regions. Projection-to-latent-structure discrimination analysis (PLS-DA) could distinguish samples of Zhejiang regions from those of other regions. Orthogonal-projection-to-latent-structure discrimination analysis (OPLS-DA) provided clear discrimination between G. lucidum samples cultivated in Zhejiang and that from other regions, in which Polysaccharides and D-galactose could be considered as candidate biomarkers. In addition, the intraspecific differentiation of G. lucidum was preliminarily investigated with samples from Shaanxi region. They were classified into four groups by PCA and PLS-DA, in which L-rhamnose, D-xylose, L-arabinose, and mannose were considered as potential chemical markers. These preliminary results contributed to our understanding of the variance of polysaccharides in Ganoderma spp. from different geographic origins and the intraspecific differentiation from the same region, which suggest great potential in the quality control of Ganoderma spp. • The acidic hydrolysate of Ganoderma lucidum polysaccharides was analyzed by HILIC-ELSD/ESI-TOF/MS. • Multivariate analysis of polysaccharides could discriminate G. lucidum origins. • Polysaccharides and Gal were candidate biomarkers for samples from Zhejiang and other regions. • Four monosaccharides could be selected as intraspecific differentiation markers. [ABSTRACT FROM AUTHOR]