Abstract Papaya is a nutritious fruit cultivated worldwide under suitable climate conditions. This plant is polygamous, bearing female, male, and hermaphrodite sex types determined by sex chromosomes XX, XY, and XYh, respectively. In this paper, a molecular sex determination of papaya var. ‘Maradol’ was carried out based on PCR and specific primers. Specific molecular markers resulted in sixty-nine hermaphrodites and twenty-one female plants, matching 100% to the flower morphology. Nevertheless, since the summer stressing conditions rose in the greenhouse, sex reversal to male phenotype was observed in 43% of hermaphrodite plants due to high-temperature conditions. A specific male marker could not detect that change, supporting the proposal that sex reversal is caused by harsh environmental conditions aimed at epigenetic modification and genes related to hormones. Our study demonstrates the effectiveness of molecular sex determination and the importance of controlling the growing requirements of papaya to avoid sex reversal.