In this work, a kind of genistein magnetic imprinted polymers (Gen-MMIPs) was successfully synthesized via surface molecular imprinting technique, in which genistein (Gen) and Fe 3 O 4 were used as the template molecule and the carrier, respectively. The obtained Gen-MMIPs were characterized by TEM, VSM, FT-IR, and XRD. The adsorption capacity of Gen-MMIPs for Gen is 33.23 mg/g, with the kinetic adsorption of Gen-MMIPs reaching equilibrium in 30 min. The imprinting factor (α) is 2.15, which indicated that the Gen-MMIPs had good selectivity, high binding capacity. The Gen-MMIPs were evaluated to separate genistein from the crude sample of Flemingia philippinensis Merr. et Rolfe, which showed that the Gen-MMIPs can be applied to separate genistein from complicated samples of natural products. These results indicated that the Gen-MMIPs have great potential for efficient separation and enrichment of genistein in complicated samples.