• Y. lipolytica enhanced β-1,3-glucanase, SOD and APX activities of mandarins. • MDA content of mandarins was decreased induced by Y. lipolytica. • Transcriptome analysis of mandarins induced by Y. lipolytica was investigated. Yarrowia lipolytica can effectively control blue mold and green mold decay of mandarins (Citrus reticulata), and the potential physiological mechanisms underlying this efficacy were examined in our previous research. The molecular mechanisms related to the resistance response, however, were not clearly elucidated. In the present study, the molecular mechanisms associated disease-resistance response induced by Y. lipolytica in mandarins were investigated. Results indicated the activity of disease-resistance related enzymes, including β-1,3-glucanase, superoxide dismutase, and ascorbate peroxidase was enhanced in mandarins when they were treated with Y. lipolytica , while malondialdehyde content decreased. Notably, based on transcriptome analysis, it was found that Y. lipolytica induced the up-regulation of genes related to the synthesis of resistance-related compounds; key genes associated with plant-pathogen interactions; reactive oxygen species scavenging genes; and genes involved in the jasmonic acid, salicylic acid and ethylene signal transduction pathways in mandarins. Y. lipolytica also down-regulated the expression levels of genes encoding cell-wall-degrading enzymes. Elucidating the molecular mechanisms associated with the biocontrol efficacy of Y. lipolytica will contribute to its potential use as an effective biocontrol agent against post-harvest diseases of mandarins. [ABSTRACT FROM AUTHOR]