Sex determination at an early stage is vital in papaya fruit production. Over time, several methods of sex determination in papaya plants by molecular markers have been developed and applied. In the present study, papaya sex-specific molecular markers and root morphology were applied for sex determination. The results demonstrated that, among molecular markers for sex discrimination, the molecular marker W11 could accurately determine the male/hermaphrodite sex from the seedling population with 100 % accuracy. Further, sex-specific molecular markers such as PMSM, pH, and Cpsm31 did not provide specific sex differentiation as previously reported. Additionally, the analysis of the root morphology of young papaya plants showed a weak correlation with sex. Considering these findings, it was concluded that a molecular marker is an accurate tool for determining the male/hermaphrodite sex from female papaya plants at an early stage.