Microstructures of FePt films deposited on MgO and MgAl2O4 single crystalline substrates were studied using aberration corrected scanning transmission electron microscopy (STEM). The [100] and [010] variants of L10-FePt were observed in-the-plane of the FePt grains deposited on the MgAl2O4 substrate, which causes in-plane component in magnetization curves. The d-spacing of the (002) planes of L10-FePt deposited on MgAl2O4 is larger than that deposited on MgO. The reduction of lattice mismatch between FePt and the substrate results in the formation of out-of-plane tensile strain leading to increase in d002 and the formation of the in-plane variants in the L10-FePt grains.