Phaseolus vulgaris L. is one of the most consumed and documented legumes in regard to its grain composition, but little is known about P. coccineus L. To evaluate and compare the phenolic compound content and antioxidant activity between landraces of P. coccineus and P. vulgaris, a total of 14 accessions of P. coccineus and P. vulgaris were collected from farmers in Oaxaca, Mexico. Based on reference standards and spectrophotometry, the polyphenol, flavonoid and anthocyanin contents were quantified, and the antioxidant activity was determined by the 2,2-diphenyl-1-picrylhydrazyl (DPPH) method. The results showed significant differences (p ≤ 0.05) between species and accessions, where P. coccineus and P. vulgaris significantly differed in their contents of polyphenols, flavonoids, and anthocyanins, as well as their antioxidant activity in the seed coat and cotyledons. Higher concentrations were found in the seed coat than in the cotyledons for both species. P. vulgaris had a higher anthocyanin content in the seed coat and a higher flavonoid content in the cotyledons than P. coccineus, but it did not for the other compounds tested. There was high variability among the accessions that were classified into four phenotypic groups: Two of P. coccineus, one of a P. coccineus–vulgaris mixed group, and one group of P. vulgaris.