The interfacial microstructures and joint strength of friction stir spot welded 6061 aluminum alloy/zinc coated steel joints were investigated using scanning electron microscopy (SEM), a tensile shear test and a micro-tensile shear test. As tool rotation speed or tool load increased, the joint strength increased to be over 5000 N in shorter process time, which was almost the same strength with plug fracture of the joint. The observation of the cross section and the fracture surface of joints showed that fracture mode of the joint was classified into three regions; region 1 of the center-jointed region, region 2 of the liquation cracking of aluminum-zinc region, and region 3 of the circumference-jointed region. The micro-tensile shear test was also performed in order to evaluate the strength at each region by preparing the samples wire-cut from several regions of the joint. The micro-tensile shear test revealed that region 2 causes the decrease of the joint strength.