Background: Phaseolus vulgaris L. is widely studied for its bioactive compounds and nutritional properties while minimal attention has been given to P. lunatus L. or P. coccineus L. Here, a comparison of the phenolic compounds, minerals and antioxidant activity between landraces of P. lunatus and P. coccineus was made based on samples from populations cultivated by indigenous communities in Oaxaca, Mexico and with reference to improved varieties of P. vulgaris. Methods: The phenolic compound contents and antioxidant activity in four samples of P. lunatus, four of P. coccineus and four improved varieties of P. vulgaris (control) were evaluated by spectrophotometry using reference standards. Through inductively coupled plasma-optical emission spectrometry, the mineral macro- and microelements contents were determined. Result: Except for Fe, Zn and Na, significant differences and high levels of variability were observed in the phenolic compound and mineral contents and antioxidant activity of P. lunatus, P. coccineus and P. vulgaris across the populations evaluated. The highest concentration of phenolic compounds was recorded in the seed coat, followed by whole grains and cotyledons.