The effect of material locations on the properties of friction stir welding (FSW) joints of two dissimilar aluminium alloys was investigated by experiments. The result of the microstructural analysis shows that the material mixing patterns in the FSW joints are quite different depending on the locations of the base metals. For the given aluminium alloys, the materials were more properly mixed when the 5052-H32 aluminium alloy was in the advancing side and the 6061-T6 aluminium alloy was in the retreating side than the case of the 6061-T6 aluminium alloy in the advancing side and the 5052-H32 aluminium alloy in the retreating side. The lowest value of the microhardness measured in the heat affected zone (HAZ) of the 5052-H32 aluminium alloy side for the both FSW joints explains why the quasi-static tensile test specimens were fractured at the 5052-H32 side of joint for the both FSW joints.