For microstructural analysis of a friction stir welded (FSWed) joint of advanced high-strength steels, dual phase (DP) and complex phase (CP) steels, are studied. FSWed joints are successfully fabricated in the following four cases: (i) DP/DP; (ii) CP/CP; (iii) DP/CP, where the advancing side is DP and the retreating side is CP; (iv) CP/DP, where the advancing side is CP and the retreating side is DP. The stir zone (SZ) of (i) the DP/DP joint mainly consists of lath martensite, while the stir zone of (ii) the CP/CP joint consists not only of lath martensite but also of bainite. In the case of (iii) DP/CP and (iv) CP/DP, they exhibit a similar microstructure including acicular-shaped phases in the joints; however, cross-sections of the joints show differences in material mixing in each case. In (iv) the CP/DP joint, temperature towards the CP steel is sufficient to cause softening, thus leading to better mixing than that in (iii) DP/CP. The phases of the SZ in each of the four cases are formed by phase transformation during the FSWed process; however, the transformed phase volume fraction of CP steel is lower than that of DP steel, indicating that dynamic recrystallization occurs mainly in CP steel. The hardness values of the SZ are significantly higher than those of the base materials, especially, the SZ of (iii) the DP/CP joint has the highest value due to highest fraction of lath martensite.