Probiotics play an important role to improve yogurt characteristics and increase its health benefits properties. The effects of adding micro-encapsulated Lactobacillus sp. and Streptococcus to yogurt in addition to natural dye obtained from (Morus rubra) were investigated. The micro-encapsulated Lactobacillus sp. and Streptococcus sp. were added to yogurt and natural dye to determine antioxidant activity, acidity, protein content and viscosity. The results showed that the use of micro-encapsulated Lactobacillus caseiLC12, Lactobacillus acidophilus LA5 and Lactobacillus rhamnosus LR22 remarkably maintained and increased the antioxidant activity as well as they decreased the undesired changes in yogurt properties involving acidity, protein content, syneresis and viscosity compared to the use of non-encapsulated strains. The data indicated that the use of Streptococcus improved yogurt characteristics which significantly lower than Lactobacillus sp. Finally, the addition of probiotics were accompanied by natural dye to yogurt remarkably increasing the beneficial healthy properties on antioxidant, acidity, protein content and viscosity. It is indicated that the priority using Lactobacillus sp. was better than Streptococcus sp.