Flaxseed mucilage and its derivatives have been extensively investigated over the last decade, mainly due to their inherent techno-functional (thickening, gelling, interface-stabilizing, and film-forming) properties that are relevant in the food industry. Hydrocolloids are used to modify food properties, such as for stabilization and emulsion, and are also used to control the microstructure of the food. Increasing research attention has been paid to the application of hydrocolloid materials in gel particles for encapsulation or texture control in food, pharmaceutical, cosmetic, and probiotic products. Thus, it is important to investigate the properties of hydrocolloids manufactured from various sources and explore their possible applications in the food industry. The applied nature of the study of plant mucus substances is associated with the ever-increasing demand for their use in the food, cosmetic, and pharmacological industries, determining the related research priorities, including the development of the most effective methods for the extraction of glycans and the search for highly productive raw materials for the production of polysaccharides. The aim of this work was to study varietal differences in the compositions of heteropolysaccharides in the mucus samples of oilseed and fiber flax varieties using a modern methodological approach for obtaining glycans based on the ultrasonic extraction of polysaccharides. The seeds of 10 flax varieties were studied, differing in their morphotype, place, and time of creation. The obtained results indicated significant differences in the quantitative and qualitative compositions of the heteropolysaccharides of flax seeds of various varieties. The contents of reducing sugars in the studied varieties ranged from 5.61 ± 0.01 to 18.81 ± 0.01 mg/g, indicating significant differences in the structural organization of glycans in different flax varieties. Additionally, the results obtained here allowed us to conclude that the range of reducing sugars for flax heteropolysaccharides is significantly less than this range for oilseed flax varieties. The obtained results of the study of the composition of flax seed heteropolysaccharides allowed us to consider them as selection trait and genetic markers.