Sago palm is flowering and fruiting just once in their life cycle. Sago palms that grow naturally and semi cultivated were generally occurred natural pollination to form fruits and seeds, if not cut down to take the starch contained in their trunk. Sago palm pollination may occur as self-pollinated and cross-pollinated. If cross-pollinated was occurred in the pollination process, it will be varied of their progenies. This study aims to reveal the genetic variation of sago palms progenies with naturally pollinated process. The research method is to collect seeds from one parent trees that have produced ripe fruit. Fruit seeds germinated to be made and tested genetic variation using RAPD markers. Isolation of DNA is done by using the fresh young leaves. DNA amplification is done by using RAPD primers. The results showed that the progenies derived from naturally pollinated of sago palms were genetically varied based on RAPD markers and also varied based on morphological phenotypic. Variations occurred in the progenies of sago palm indicated that the sago palms were estimated cross-pollinated naturally, as a result fruits and seeds with genetically differences.