Several Amaranthus vegetables (Amaranthaceae) have been recognized as valuable sources of minerals, vitamins, proteins, and phytonutrients, with health-promoting characteristics. In this study, three edible Amaranthus species, namely A. hybridus (AH), A. blitum (AB), and A. caudatus (AC), were chemically characterized using non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique. Further, multivariate chemometric analyses were conducted, including principal component analysis (PCA) and correlation-covariance plot (C-C plot). As a result, forty-one diverse compounds were identified, which varied in distribution and abundance across the investigated species. Amino acids and flavonoid glycosides were the most prevalent metabolites. Other identified compounds comprised nucleoside, chlorogenic acids, hydroxy cinnamoyl amides, and triterpenoid saponins. The most discriminant metabolites were flavonoid glycosides and hydroxy cinnamoyl amides, giving each species a chemotaxonomic identity. Advancing the chemotaxonomy of Amaranthaceae, adenosine nucleoside and N-coumaroyl-ʟ-tryptophan were first reported from this family. Isorhamnetin and tricin glycosides were uniquely identified in AC, offering useful chemotaxonomic markers for this species. Notably, AB and AH profiles shared most metabolites, yet with varying abundance. These include adenosine, nicotiflorin, dicaffeoylquinic acids, and N-trans-feruloyl-4-O-methyldopamine. However, N-coumaroyl-ʟ-tryptophan and kaempferol dirhamnoside were exclusively found in AB, separating it from AH. In conclusion, the applied analytical techniques established molecular fingerprints for the included species, identified specific 
biomarkers, and investigated their interconnections.