This work aimed to characterise Moringa oleifera (Mo) and Moringa peregrina (Mp), grown in Saudi Arabia, based on nutritional and molecular markers. Seven genotypes per species were evaluated using 1-year-old trees. The nutritional characterisation included chlorophyll, protein, macronutrients, micronutrients, and heavy metals. Simple sequence repeat (SSR) was applied using nine primers for genetic characterisation. Significant differences in nutritional content were found between the two species and among the genotypes of each species. Mp had more chlorophyll content, however Mo contained higher protein, Fe and Zn. Correlations among nutritional characteristics allowed representative classification of genotypes based on these pertinent indicators only. Cluster analysis separated the genotypes of each species in independent group, but three Mo genotypes and two Mp genotypes were distinguished for their variability in nutritional properties. Most Mo genotypes amplified the nine SSR primers, however 6/9 primers only produced bands in Mp genotypes. The number of amplified primers per Mp genotype varied from zero to six. A strong relationship was found between nutritional and molecular classifications of genotypes. The efficient classification based on four chemical characteristics could be beneficial for Moringa evaluation. The correlation between genetic and nutritional variability could serve in improving Moringa and identifying genetic criteria.