The application of probiotics in aquaculture represents a promising alternative for disease prevention. These microorganisms must survive adverse conditions during handling and storage to be administered in high concentrations to the host. This is especially important when stressful conditions, such as low water contents, are present in animal feed. Bacterial encapsulation has been used to maintain probiotic viability in human food; however, the usefulness of the encapsulation techniques in animal feed needs to be evaluated. In the present study, optimal conditions for encapsulation in alginate of a fish probiotic Shewanella putrefaciens strain (Pdp11) have been determined. Different alginate (1%, 2%, 3% and 4% w/v) and calcium chloride (0.5%, 1% 2% and 3% w/v)concentrations were used to elaborate alginate beads. The results obtained indicate that S. putrefaciens Pdp11 can be encapsulated successfully in calcium alginate beads. The percentages of encapsulated cells were above 80%, the lowest efficiency rates corresponding to high calcium availability (3%). In addition, capsules containing viable S. putrefaciens Pdp11 can be stored at 4 °C for at least 1 month, survival rates being above 90%. On the contrary, storage of the capsules at 22 °C resulted in 40% viability loss within 30 days. Finally, the survival of encapsulated probiotics through fish gastrointestinal tract has been demonstrated.