This paper reports the magneto optical Kerr effect (MOKE) study of magnetic thin film (of Permalloy-Py) deposited on molecular self-assembled monolayer (SAM) of different organic functional groups (OFGs), polar (-COOH/NH2) and non-polar (-CH3) on Au and Si/SiO2 substrates. MOKE study of these hybrid films demonstrated the change in magnetic behavior of Py due to its initial uniform growth on polar SAM and cluster like growth on non-polar SAM. Clear difference in MOKE response in terms of coercivity, shape of hysteresis loops, and even paramagnetic response was observed for ferromagnetic thin film (similar to 5 nm) of Py deposited on polar and non-polar SAM. For thick (similar to 10 nm) film Py deposited on SAM MOKE hysteresis loops were almost square on all SAM (polar and non-polar) with some difference in coercivity due to observed contrast in initial morphology arising from the difference in reactive nature of the OFG of SAM. These results suggest an alternative way for tuning the magnetic properties of the ferromagnetic thin film by OFG of SAM. Furthermore, with patterning flexibility of SAM at micron/nano scale, these finding can be used to create template of magnetic thin film. (c) 2012 Elsevier B.V. All rights reserved.