Large-eddy simulation (LES) of three-dimensional non-premixed hydrogen flames in a confined annular configuration has been conducted in order to clarify the interactions between different instabilities and swirling motion in the reacting jet flow field. The LES approach in parallel implementation follows a dynamic k − Δ subgrid-scale (SGS) model in which the SGS stress is modelled by the eddy viscosity hypothesis using the sub-grid scale turbulent kinetic energy. The results show a geometric central recirculation zone because of the bluff body configuration and a near-wall recirculation region for all the cases considered. The swirling flames also developed a toroidal recirculation zone with a collar-like shear structure around it that ended up in a vortex-breakdown bubble (VBB) for the case of moderate swirl number. As the degree of swirl was increased, the VBB increased in size and strengthened up to create a large central recirculation zone. It was shown that these regions with flow reversal enhance the air and fuel mixing and thus, improve the entire combustion process.