The genus Moringa is a phenotypically varied group of trees and shrubs, widely distributed in the tropical and subtropical regions, whose species are mostly sought after for nutritional, nutraceutical and industrial use. The Namibian Moringa ovalifolia consists of phenotypically different populations scattered across the country and occurring in different ecological systems. In the present study, species boundaries of the Moringa ovalifolia from Halali, Uis, Sesfontein, Sprokieswoud (Etosha) and Namib Nauflukt Park were assessed using internal transcribed spacer sequences of nuclear ribosomal DNA data. In order to reconstruct the phylogenetic relationships of the populations under investigation, Cylicomorpha parviflora Urb. was used as an out group to root the phylogenetic trees. Results from all the phylogenetic analysis methods used in this study, provided evidence for one monophyletic group for all the Namibian Moringa ovalifolia populations. All the three phylogenetic analysis methods inferred that the Namibian Moringa ovalifolia is a sister clade to other Moringa species. Furthermore, the Moringa ovalifolia from different Namibian populations nested together in all analyses forming a monophyletic clade, inferring a relatively recent separation from each other. The results demonstrate that the different populations of the Namibian Moringa ovalifolia are phylogenetically similar despite their morphological differences and geographic isolations. Keywords: Internal transcribed spacer, Monophyletic clade, Moringa ovalifolia, Phylogenetic trees, Species boundaries, Specimens.