Amaranthus species are widely cultivated as dietary crops and are promising sources of phytochemical compounds with antioxidant properties. To explore Amaranthus as a potential medical resource, 289 accessions (nine species) were cultivated, and their agricultural characteristics, total phenolic content (TPC), rutin contents, and antioxidant activities [2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS)] were studied. Wide variations in agricultural traits, phytochemical contents, and antioxidant activities were observed between the accessions and across species. The effects of agricultural traits were evaluated, and the results indicated that yellow-flowered amaranth genotypes could be important because of their high values of TPC, rutin contents, DPPH, and ABTS. In addition, leaf length, days until 50% flowering, days until 50% heading and days until maturity, showed positive correlations with TPC, rutin contents, DPPH, and ABTS. The whole dataset was subjected to principal component analysis, and distinctive aggregation was observed across the Amaranthus species. In total, 289 accessions were clustered into three groups, and seven genotypes were determined as being good medical resources due to their high phytochemical content and antioxidant activities. Our findings provide important information for the development of new varieties with high phytochemical contents and high levels of antioxidant activity.