Summary There is a growing need for new formulations of carriers with better protection for bacterial inoculum. One of the newer techniques in inoculum making is encapsulation method. With this method, the whole bacterial cells are immobilized in defined space – matrix, where the cells are protected from environmental activities before use. Encapsulation of the inoculum was performed with ionic gelation method. The alginate-based microparticles (500-600 µm) containing viable B. japonicum strain were solidified in CaCl2. The initial number of viable bacteria in every sample was 9.0 log CFU/ml. Chitosan coated particles had a higher mortality rate than non-coated particles, with 1.3 log CFU/ml in lyophilized and wet microparticles stored at room temperature. High viability of B. japonicum was registered in wet particles stored at constant −20°C for thirty days with a viability rate of 8.84 log CFU/ml.