In this research a multidisciplinary approach was used to unveil the genetic, metabolic uniqueness and relationships of endemic Mascarene Aloes (Aloe macra, Aloe purpurea, Aloe tormentorii)withrespectto Aloe vera.Nuclear magnetic resonance spectroscopy, DNA sequencing and antioxidant profiles of these Aloes were studied. Principal component analysis following 1 H NMR revealed the specificity of the Mascarene Aloes relative to Aloe vera. The superior free radical scavenging ability of A. purpurea, A. macra and A. tormentorii as compared to other Aloes was also unveiled. Phylogenetic analyses of chloroplast genes and ITS region sequences of these Mascarene Aloes were done using maximum parsimony and Bayesian analysis. Mascarene Aloes clustered within one clade separate from Aloe vera confirming their relative recent emergence in this genus. Results from this study showed that there is sufficient evidence at the metabolomic and molecular level to distinguish between Aloe purpurea from Mauritius and that of Reunion.