In this study flaxseed mucilage (FM) was used for co-encapsulating probiotic Lactobacillus caseion the alginate (ALG) matrix. For this purpose, FM was extracted and its physicochemical properties were evaluated. Then, the effect of FM (0, 0.3, 0.6, 0.9, 1.2 and 1.5%) on the growth of L. caseiin MRS broth was investigated. Finally, L. caseiwas encapsulated by a mixture of ALG (1, 2, and 3%) and FM (0 and 0.9%) using the emulsion technique and the stability and survival rate of the probiotic in simulated gastrointestinal conditions were studied. The results showed that FM had a relatively low apparent viscosity (42 ± 2.3 mPa s) and the most important monosaccharides in its structure were xylose, galactose and arabinose. FM positively affected the growth of L. caseiin MRS broth and 0.9% FM showed the highest viable bacterial count. After encapsulation, the created microcapsules exhibited spherical morphology with an encapsulation efficiency (EE) of higher than 95%. The mean diameter of the created microspheres significantly increased by increasing the ALG concentration and incorporation of FM (P < 0.05). The addition of FM during microencapsulation increased L. caseiresistance against the harmful effects of the simulated digestive system. The least logarithmic cycle reduction during passage through simulated gastrointestinal conditions was seen in the 3% ALG + 0.9% FM and 2% ALG + 0.9% FM. It can be concluded that the addition of FM into ALG microcapsules can improve the survival of L. caseiunder gastrointestinal conditions.