Abstract: Background and Objective: Amaranthus hybridus and Amaranthus spinosus are widely distributed in Nigeria and are being used as medicinal plants. The comparative morphological, anatomical and phytochemical studies were carried out on 2 species of the genus Amaranthus L. (A. hybridus and A. spinosus) to determine their differences to easy their identification and potential sources of raw materials for pharmaceuticals. Materials and Methods: Standard HPLC method was used for phytochemical screening. For anatomical study, fresh specimens were dehydrated, wax embedded, sectioned, mounted and micro-photographed using Optika B-1000 FL LED fitted with digital camera and morphological study was done by visual observation. Results: The presence of spines on A. spinosus distinguishes it from A. hybridus. Also, the stem of A. spinosus is reddish-brown while that of A. hybridus is light green. The number of vascular bundles in the midrib, petiole, stem and root were different and could be used to differentiate them. Data obtained from the quantitative phytochemical analysis showed that their concentrations varied among the 2 species. Amaranthus hybridus had 72.56 and 61.79% vitamin A in the root and leaves, respectively while compared to A. spinosus. Leaves of A. hybridus had higher total flavonoids concentration of 56.46% while A. spinosus had the highest phenolics of 19.27 g/100 g and 18.63 g/100 g in the leaves and roots, respectively. Also, the roots of A. spinosus had the highest concentration of alkaloids, glycosides and phenolics. These explain why they are used in ethno-botany in Nigeria. Conclusion: Based on the phytochemical constituents, both plants could be valuable sources of dietary vitamins and potential sources of phytochemicals if properly exploited.