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In this study, yeasts isolated from citrus groves, trees and leaves were identified, phylogenetic analyzes were performed and their antifungal effects were determined. Wickerhamomyces anamolus (M72), Meyerozyma guilliermondii (M77), and Pichia kudriavzevii (M74) species were identified and were found to have antifungal effects against P. digitatum and P. italicum. Pichia kudriavzevii (M74), which has the highest antifungal effect, showed 67% and 62% inhibition rates against P. digitatum and P. italicum, respectively. An encapsulation study was carried out using a microencapsulation process to ensure that the M74 strain, which has the most antifungal effect, is long-lived enough to be a biopesticide. The optimum spray drying process parameters as well as the optimum concentration values of wall materials were investigated in the spray drying process for the microencapsulation of Pichia kudriavzevii (M74) through the Taguchi methodology. The formulation containing 0.1% sodium alginate (SA) and 10% corn starch (CS) showed a good performance in the inhibition of P. digitatum, a mold that causes losses in orange, thanks to its high percentage of viability (73%). The inhibition percentages may indicate that this formulation may be a candidate to be considered as a potential alternative application to synthetic fungicides on orange fruits for the effective control of P. digitatum mold.