The microstructure and mechanical properties of friction stir spot welding of ultrahigh strength dual phase (DP) and complex phase (DP) steels are compared based on the experimental results. For both DP and CP steels, FSSW joints are successfully fabricated using the same process parameter set. While the microstructure of joints are characterized in detail using scanning electron microscopy, electron back scattered diffraction, and transmission electron microscopy, the mechanical property of joints are evaluated by shear tensile tests. The result of the microstructural analysis shows that the stir zone (SZ) of CP steel mainly consists of bainite and martensite, while no bainite is identified in the SZ of DP steel. The existence of bainite in the SZ of CP steel suggests that the cooling rate, which is nearly identical for both CP and DP steels, was not fast enough to suppress the effect of the alloying composition, particularly that of Mn, on the phase transformation. The result of the present study contributes to the development of solid state joining process of the ultrahigh strength steels.