Stability analysis of stratified multiphase flow for a spanwise system of rotation plays a pivotal role in micromixing and micromachines. In several such systems, centrifugal actuation is the driving force, which creates a pressure gradient in a rotating channel and Coriolis force enhances mixing in a short span by destabilizing the flow. Here, we focus on the impact of the Coriolis force on a rotating two-fluid flow through a microchannel, which is miscible in nature, having small viscosity difference and thereby forming a thin diffusive interface between fluids due to viscosity stratification. Modal stability analysis is used to estimate the critical flow parameters which are, in turn, responsible for regulating the instability mechanism for different viscosity contrasts and mixed layer thicknesses. Usually, viscosity stratified flow with respect to streamwise disturbance becomes more unstable for a thinner mixed layer. On the contrary, our numerical computation confirms a completely discrepant scenario by considering Coriolis force-driven instability of a miscible flow system on account of spanwise disturbances. Possible physical mechanisms for the same are discussed in terms of base flow pattern and the energy fluctuation between the perturbed and base flow. Comparison of three-dimensional disturbances of the flow field, in both clockwise and anticlockwise directions (for two different viscosity ratios), is executed to provide an insight into the dynamics of the flow system. Distributions of the velocity perturbations display a critical bonding between the vortices near and away from the mixed layer. These vortices are, in turn, responsible for the variation in instability mechanism with respect to different viscosity ratios and rotational directions. © 2019 American Physical Society.