The main goal of this study was to develop an improved oral delivery system for Pediococcus pentosaceus OZF, a promising probiotic bacterium, and to assess its viability under simulated gastrointestinal (GI) tract model by comparing the efficiency of microbiological and molecular approaches. Encapsulation was carried out using extrusion method and as a result, encapsulation system including 0.75 % lactulose, 1.8 % sodium alginate, 0.1 M CaCl2, and 5 min gelling time was shown to have a significantly protective effect against pH 2.0 acid stress over 3 h. However, completely loss of viability was exhibited by free OZF cells under similar conditions. To provide an additional barrier for capsules, coating process was investigated using different biopolymers, and the survival rates of free and encapsulated OZF cells upon expose to simulated GI conditions were detected by conventional culture techniques and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) method. No significant differences between the biopolymers were detected, except the chitosan which leads totally 85 % protection and extra 25 % improvement in the survival of OZF cells compared to uncoated capsules. In conclusion, our findings indicated that chitosan-coated capsules provided an important protective effect on the viability of OZF cells against the GI system conditions encountered during the transit of food. In addition, this study was found successful in monitoring the viable OZF cells in capsules using PMA-qPCR method.