© 2019, Springer Science+Business Media, LLC, part of Springer Nature. We evaluated the cytotoxic and genotoxic effects of protein isolates of ayocote beans on adult male CD1+ mice and the anticancer activity of their protein fractions using SiHa Cells. The mice that received protein isolate showed a Polychromatic Erythrocytes (PCE) increase at 48 h; a significant PCE decrease was observed in mice administered the protein isolate-Daunorubicin (isolate-DAU) mix. A micronucleated erythrocytes (MNE) increase was observed in mice that received the mix in all times tested. All protein fractions of ayocote beans (black and purple) showed inhibition against SiHa cells proliferation at doses of 3000 or 5000 µg/mL. The maximal inhibitory concentration (IC50) of each protein fraction was reached at a concentration of 5000 µg/mL. A synergistic effect of isolate-DAU was observed in the in vivo test; the effect of the protein fractions on SiHa cells proliferation depended of the ayocote bean variety used.