The role of hydrodynamics resulting in the mixed-mode oscillations (MMO) of unsteady pressure in a backward facing step combustor with partially premixed flame is investigated using time-resolved particle image velocimetry and CH* chemiluminescence imaging. This mode of pressure oscillations comprises switching between high-amplitude oscillations dictated by acoustic mode and/vortex mode and low-amplitude oscillations. The high-amplitude oscillations are marked by intense flow and flame modulation, while the low-amplitude oscillations are accompanied by small-scale structures on the shear layer, that are sedate in driving the heat release oscillations. The small-scales override on the elongated flame that resides in the recirculation zone of the step. The key aspect of the present work is in identifying the transitional events that result in the decay/ onset of high-amplitudes. This is achieved by tracking vortex cores at each instant during the transition. The small-scale shear layer structures, that are present during low-amplitude events merge as they convect with the flow. The identified vortex cores on the shear layer and in the recirculation zone reduce in their multiplicity as the merger progresses. This subsequently results in the genesis of a large-scale structure that modulates the flame coherently, thereby triggering high-amplitude oscillations. This is corroborated with identifying the presence of a single vortex core resulting in high amplitude events. © 2020 The Combustion Institute. Published by Elsevier Inc. All rights reserved.