The aim of this study was to explore the diversity of yeasts in the orangery of Beibei Chongqing and their potential for biological control of Penicillium digitatum on oranges. Yeasts were isolated from the surface of fruit, leaves and soil in three citrus orchards in this district. The yeasts were identified by PCR amplification and partial sequencing of internally transcribed spacer (ITS) regions and 5.8S ribosomal DNA (rDNA). The 71 yeast isolates belonged to 8 genera: Metschnikowia, Pichia, Candida, Pseudozyma, Kazachstania, Issatchenkia, Hanseniaspora, and Barnettozyma. All yeast isolates were tested for the inhibition of green mold on potato dextrose agar (PDA) medium, and 45 isolates reduced the growth of fungal mycelium as shown by inhibition zone formation. Twelve isolates were tested for antagonistic activity against Penicillium digitatum on navel oranges, and the biocontrol activity of the various isolates in reducing disease incidence ranged between 26% and 93%. In particular, Metschnikowia sp. FL02 completely inhibited the occurrence of green mold rot on the seventh day after inoculation. The results of this study suggest that antagonist yeasts frequently found on leaves and fruit in Beibei Chongqing orangery have potential for inhibiting citrus green mold.