Non-target effects of two broad spectrum, foliar spray, systemic fungicides, Amistar (azoxystrobin 25% EC) and Score (difenoconazole 25% EC) in terms of cytotoxicity were investigated at concentrations ranging from 0.44 - 2200 μg (a.i.) mL-1. The test material used was the root meristems of Allium cepa. At the recommended dose for field application (2.2 μg (a.i.) mL-1), Difenoconazole depressed mitotic index by 4.305% while Azoxystrobin showed a decrease of 1.282% over untreated control at 12 h exposure period. The extent of chromosomal abnormalities has direct relationship with the concentration of the active ingredients and treatment time. The fungicide treated root meristems tended to recover from the cytotoxic effects when they were transferred to distilled water. The rate of recovery as indicated by increasing mitotic index and decreasing incidence of cytological abnormalities was highly pronounced in Azoxystrobin treated roots when compared with those treated with Difenoconazole.