Amaranthus is a cosmopolitan genus comprising large number of species with many morphotypes cultivars/accessions having diversified morphological features. The species, morphotypes within Amaranthus are very closely related requiring microclassification even revision in present taxonomic status. Most of the works have been done employing grain Amaranthus and their putative ancestors applying morphological and molecular data. In present study along with morphological features, phenolic compounds (secondary metabolites), isozyme profile of acid phosphatase were applied to get comprehensive reflection of interrelationship and relative closeness among the species, morphotypes/accessions of few vegetable, grain and weed Amaranthus. Both the vegetable and grain Amaranthus are supposed to have originated from respective weed progenitor through occasional outcrossing and gradual domestication. The study strongly vouched the previous interpretations regarding interrelationship of grain Amaranthus and their derivation from their putative progenitor also showed clear separate clustering of vegetable and grain Amaranthus with their close relatives. A sharp congruence in cluster pattern was achieved between morphological dendrogram and cumulative dendrogram computed on morphological and biochemical parameters, which is a rare event in systematics.