The present study is focused on probiotic characterization of four yeasts viz. VIT-SJSN01, VIT-ASN04, VIT-ASN01 and VIT-ASN03 isolated from food samples based on their auto-aggregation, co-aggregation ability and haemolytic activity. All the yeast strains showed good self-adhering and co-adhering potentiality with a value index of greater than 85%. None of the strains exhibited haemolysis which confirmed their non-pathogenic nature. Yeast strains were encapsulated in sodium alginate, sodium alginate coated with chitosan and sodium alginate-gelatinized with starch. Size and morphology of the beads and capsules were determined using SEM analysis. Encapsulation output and viability under storage condition was investigated. It was found that probiotic yeasts encapsulated in sodium alginate beads, chitosan coated beads and microcapsules showed better survival to simulated gastrointestinal conditions compared to free cells.