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Abstract Background Jujube resources are abundant in China, and Shanxi Province in particular is one of the places where they originated. The most famous 6 geographical indication (GI) jujube species in Shanxi are often masqueraded by nonoriginal jujube species, which seriously undermines the brand image. However, the current national quality standards, which have simple indicators, cannot completely trace the botanical and geographical origin of GI jujubes. Compared with small biomolecules and genes, polysaccharides possess a complicated structure and are sensitive to their geographical location and botanical origin, and these characteristics are important for botanical and geographical traceability. Therefore, we selected the 6 most famous GI jujube species in Shanxi Province, measured and analyzed their crude polysaccharide characterizations, and then selected efficient tracing indicators. Results The crude polysaccharides from 6 GI jujube species of Shanxi Province were tested with several parameters, including their purity (the content of polysaccharides), uronic acid content, Mw distribution, monosaccharide composition, functional groups and bonds. In the assays that measured purity and uronic acid content, the purity varied within a very narrow band (96–99%) and presented no negative or positive correlation with uronic acid content. In the experiment that measured the Mw distribution by HPGPC, five peaks (RT1, RT2, RT3, RT4, RT5) were almost observed in 6 jujube species, and the RT3 content (240–250 Da), which showed a significant correlation to the content of RT4 and RT5, exhibited significant differences among 6 jujube species (RSD = 1.28 > 1.00). The monosaccharide composition indicated that the polysaccharides from 6 jujube species were rich in glucose (55–75%), arabinose (10–15%) and galactose acid (10–20%), with small amounts of rhamnose, glucosamine hydrochloride, galactose, xylose, and mannose (less than 5%). The FT-IR spectrum showed that crude polysaccharides from six jujube species shared similar functional groups and chemical bonds. Conclusions The results above indicated that in the 6 GI jujube species, both homogeneity and differences were observed in the Mw distribution of crude polysaccharides. First, five peaks (RT1, RT2, RT3, RT4, RT5), which represent the Mw of 186,646–285,262 Da (RT1), 4634–17,296 Da (RT2), 240–250 Da (RT3), 98–103 Da (RT4) and 57–64 Da (RT5), respectively, could be detected in all 6 jujube species. Second, the RT3 contents exhibited significant differences among the 6 jujube species (RSD = 1.28 > 1.00) and showed a significant correlation with RT4 and RT5. Therefore, the Mw distribution may be treated as a potential distinguishing indicator among the 6 jujube species. Graphical Abstract |