Objective To evaluate the possible protective role of honey formed through innovative way by using magnetized water instead of tab water in supplementary feeding for bees (HW) and compared with two honey types formed by two different feeding solutions; sugar syrup (HS) and nectar of flowers (HF) against cyclophosphamide (CP) genotoxicity in mice bone marrow cells, by using the micronucleus assay (MN). Methods Mice were divided into 8 groups from 3 animals each. G1 as control. G2 were exposed to CP (40 mg/kg), G3, G4, and G5 received two dose of three types of honey at doses (300, 600 mg/kg) respectively. The other groups G6, G7 and G8 were supplemented with three types honey (300 mg/kg) in three different experimental protocols, as pre 2 h, post 2 h, and concomitant treatment for 7 and 14 days. Results Examination and analysis of MN showed no mutagenic effect of three types honey per se doses, especially in low dose (300 mg/kg). Meanwhile, CP induced a significant (P < 0.01) increase in MN frequency. While dual treatment with groups of honey HW caused a significant reduction in MN induced by CP in bone marrow cells in a time-dependant manner. Also, the results confirmed the protective efficacy of HW group and/or HF group as compared with HS group, against CP-toxicity. Conclusion Our study suggests using magnetized water in supplementary feeding of bee, that could give the honey protective effect against genotoxicity induced by CP, it is also fosters antioxidant activity of honey constituents. Therefore, honey HW can be used as an adjuvant with chemotherapeutic agents for minimizing the genotoxic side effects of the anticancer drug CP.