To increase the knowledge about Stevia rebaudiana variability and to develop a breeding strategy through hybridizations and selection to get cultivars adapted to Egyptian conditions. We performed hybridizations for three Stevia varieties with half-diallel design then studied the molecular and phenotypic diversity. Based on leaf dry weight, we selected the top five hybrids from each cross. From these hybrids, the top two hybrids were selected for genetic diversity assessment based on the RA/ST ratio. Molecular diversity assessment was done using ISSR and SCoT techniques. SCoT exhibited a higher discriminatory potential compared to ISSR technique. Both were effective tools for assessing genetic relationships among studied genotypes. H1-9 hybrid exhibited high values for most traits. While H1-1 exhibited exceptional performance of plant height and RA/ST ratio. The greatest molecular and phenotypic distance between parents was observed between the Spanti and China1. The H1-9 and H1-1 hybrids, resulting from the crossing of these parents, were characterized by distinct positive unique molecular markers. H1-9 was distinguished by three markers: one identified by the SCoT-22 primer and two by ISSR primers. H1-1 was distinguished by four markers: one identified by the SCoT-12 primer and three by ISSR primers. High genetic divergence values were observed between H1-9 and the other genotypes. Indicating the possibility of improving stevia in future breeding programs by crossing the H1-9 with any of the studied genotypes and utilizing these genotypes and their unique markers to achieve satisfactory improvements aligned with sustainable development goals.