The effect of microencapsulation on previously isolated Lactobacillus delbrueckii 94/L4 as starter culture for yogurt, and Lactobacillus casei 97/L3 as a probiotic candidate was investigated. Preliminary results showed that L. delbrueckii 94/L4 exhibited tolerance to bile, unlike L. casei 97/L3. Freeze drying significantly (p < 0.05) reduced the viability of both isolates by log 0.71-2.70. Although microencapsulation preserved the viability of L. casei 97/L3 cells exposed to simulated gastrointestinal tract conditions for 120 min, it did not impart significant (p < 0.05) protection against loss of viability during the first 30 min of exposure. Conversely, microencapsulated L. delbrueckii 94/L4 with the addition of Streptococcus thermophilus 24/S1 as starter culture was successfully incorporated into milk to form yogurt, yielding a significantly (p < 0.05) improved product quality.