This study aimed to assess the diversity of Moringa oleifera and Moringa peregrina in Saudi Arabia. Seven genotypes per species were characterized morphologically using 14 morphological characteristics and genetically using 10 ISSR primers. The studied genotypes were classified according to each characterization, and the correlation between morphological and genetic diversity was investigated. M. oleifera genotypes were distinguished by long, thick stems with more crown spread, and larger pinnate leaf area compared to those of M. peregrina. Plant height and pinnate dimensions were the most pertinent indicators for the discrimination among genotypes where they were correlated to all morphological characteristics and gave representative classification. Diversity was found between the two species and among the genotypes of each species. The ISSR molecular markers were effective in the characterization of genetic diversity of Moringa where the average of polymorphism across the 14 genotypes was sufficient (90.8%). Dinucleotide repeat (AC)n primers (UBC825, UBC826 and UBC827) and a trinucleotide primer (UBC864) were the best primers, regenerating the maximum number of polymorphic bands per primer (8–10) and the highest polymorphism level among genotypes (91–100%). Principal coordinate analysis showed similar classification for morphological and molecular data where the two species were separated in two main clusters with three sub-clusters per species. The association analysis showed good correlation, up to a 0.84 determination coefficient, between genetic diversity and morphological variability. The primers UBC826 and UBC827 were the most informative markers, revealing correlations with 12 morphological characteristics. The results of the present study provide valuable morphological and molecular characterizations of the two most important Moringa species. Efficient morphological classification based on three characteristics could facilitate the evaluation of diversity in Moringa. Genetic diversity could be simply assessed using the two best ISSR primers (UBC826 and UBC827). The diversity found among genotypes could be of great importance for the selection of clones with desirable characteristics for further improvements of Moringa.