One of the difficulties with bobbin friction stir welding (BFSW) has been the visualisation of microstructure, particularly grain boundaries, and this is especially problematic for materials with fine grain structure, such as AA6082-T6 aluminium as here. Welds of this material were examined using optical microscopy (OM) and electron backscatter diffraction (EBSD). Results show that the grain structures that form depend on a complex set of factors. The motion of the pin and shoulder features transports material around the weld, which induces shear. The shear deformation around the pin is non-uniform with a thermal and strain gradient across the weld, and hence the dynamic recrystallisation (DRX) processes are also variable, giving a range of observed polycrystalline and grain boundary structures. Partial DRX was observed at both hourglass boundaries, and full DRX at mid-stirring zone. The grain boundary mapping showed the formation of low-angle grain boundaries (LAGBs) at regions of high shear as a consequence of thermomechanical nature of the process.