Effect of two distinctive tool designs along with other tool related parameters including speed of traverse of tool and offset distance of tool pin during friction stir welding of dissimilar AZ91C and AZ31B alloys of Mg were investigated. Experimental recordings revealed that all the joints fabricated during 1st set of investigations employing cylindrically tapered pin geometry and their offset distances being 0.5 mm or 1mm towards any one of the parent metals possessed flaws. Joint No: II-3 fabricated in 2nd set of investigations by employing 15mm diameter inner shoulder tool with threaded cylindrical tapered pin geometry at a tool offset distance of 0 mm was found be free from flaws. This joint exhibited a tensile strength of 186 MPa which was 78.81% of AZ91C and 70.72% of another parent metal AZ31B. Existence of intermetallic phased constituents, namely, Mg17Al12 in several regions of fractured surfaces have contributed to the supplementary brittleness in the zone of nugget, and have reduced the tensile strength of the joint.