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The aim of this study was to investigate the influence of molar mass of thiolated polymers (thiomers) on their in situ gelling properties. Chitosan–thioglycolic acid (chitosan–TGA) and pectin–cysteine (pectin–Cys) of increasing molar mass were chosen to produce in situ gels in combination with carbamide peroxide. Low molar mass chitosan (∼2 kDa) was prepared by oxidative degradation with NaNO2, whereas pectin was depolymerized by heat treatment. Thiomers, displaying 1271–1616 μmol (chitosan–TGA) and 305–403 μmol (pectin–Cys) free thiol groups per gram polymer, were synthesized via amide bond formation mediated by a carbodiimide. The results showed that a reduction of molar mass combined with increased concentrations of both cationic chitosan–TGA and anionic pectin–Cys leads to higher final viscosities and to a higher relative increase in viscosity within 60 min and 180 min, respectively. Using this method, the dynamic viscosity of a very low molar mass chitosan–TGA (∼2 kDa) could be increased 100,000-fold within 60 min and 390,000-fold within 180 min. In view of these in situ gelling properties carbohydrate thiomers might be useful for various pharmaceutical applications such as vehicle for drug delivery or as wound dressing material.