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The aim of this study was to investigate the effect of bacteria strain (Lactobacillus rhamnosus and Lactobacillus plantarum) and encapsulation system (multilayer and simple emulsion) on physicochemical, stability and viability characteristics of bacteria. Particle size of LR-ME (Lactobacillus rhamnosus embedded in multilayer emulsion), LR-E (Lactobacillus rhamnosus embedded in simple emulsion), LP-ME (Lactobacillus plantarum embedded in multilayer emulsion) and LP-E (Lactobacillus plantarum embedded in simple emulsion) was measured as 10.63, 3.53, 10.47 and 4.19 μm, respectively. Results showed that the multilayer emulsion samples had larger particle size than simple emulsion. But the bacteria strain had no effects on the particle size of the samples. Span showed that the simple emulsion samples had more dispersion than the multilayer emulsions. Zeta potential of LR-ME, LR-E, LP-ME and LP-E emulsion samples was measured -51.26, -39.35, -56.65 and -30.25 mV, respectively. Multilayer emulsion samples had lower negative zeta potential than simple emulsion, but the bacterial strain had no effect on the zeta potential of the samples. Multilayer emulsion samples had higher stability than simple emulsion, But bacterial strain had no effect on the stability of samples. The bacterial counts in LR (free Lactobacillus rhamnosus), LR-ME, LR-E, LP (free Lactobacillus plantarum), LP-ME and LP-E were measured 8.49, 8.48, 8.51, 8.41, 8.37 and 8.39 log cfu/g, respectively. The results showed that coating with multilayer emulsion is the best method for increasing the viability of probiotics.