Sex identification in Dioecious plants is a crucial step during Plant breeding practices. In the absence of morphological markers it becomes difficult to identify the sex of the plant at pre-flowering stage. There is a need of development if molecular tools for the sex identification at seedling stage. This can save the time and economic sources. In this book molecular methods described for sex identification in Momordica dioica Roxb and Simarouba glauca DC. Momordica dioica is a perennial, dioecious, tuberous, semi-wild climber which is under cultivation at very few regions of India and Bangladesh. Simarouba glauca DC. is an important oil yielding, perennial, poly-gamo-dioecious tree. RAPD and SCAR markers developed in this research work can be efficiently used for the screening of male sex at seedling stage in Momordica dioica and Simarouba glauca.