This paper is focused on the genesis of microstructures in Friction Stir Welding (FSW) of the Ti-6Al-4V alloy. Several titanium joints, initially prepared with 4 different pre-heat treatments, were processed by FSW. Detailed microstructural analyses were performed in order to investigate change in the microstructure during the process. In this work, the FSW processing allows a controlled and stable microstructure to be produced in the stirring zone, regardless of the initial heat treatment or the welding conditions. The welded material undergoes a severe thermo-mechanical treatment which can be divided into two steps. First, the friction in the shoulder and the plastic strain give rise to the necessary conditions to allow a continuous dynamic recrystallization (CDRX) of the β phase. This operation produces a fine and equiaxed β grain structure. Second, once the pin has moved away, the temperature decreases and the material undergoes a heat treatment equivalent to air quenching. The material thus exhibits a β→β+α transformation with germination of a fine intergranular Widmanstätten phase within the ex-fully-recrystallized-β grains.