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Abstract The Rayleigh–Taylor (RT) instability is ubiquitously observed, yet has traditionally been studied using ideal fluid models. Collisionality can vary strongly across the fluid interface, and previous work demonstrates the necessity of kinetic models to completely capture dynamics in certain collisional regimes. Where previous kinetic simulations used spatially and temporally constant collision frequency, this work presents five-dimensional (two spatial, three velocity dimensions) continuum-kinetic simulations of the RT instability using a more realistic spatially varying collision frequency. Three cases of collisional variation are explored for two Atwood numbers: low to intermediate, intermediate to high, and low to high. The low-to-intermediate case exhibits no RT instability growth, while the intermediate-to-high case is similar to a fluid-limit kinetic case with interface widening biased toward the lower-collisionality region. A novel contribution of this work is the low-to-high collisionality case that shows significantly altered instability growth through an upward movement of the interface and damped spike growth due to increased free-streaming particle diffusion in the lower region. Contributions to the energy flux from the non-Maxwellian portions of the distribution function are not accessible to fluid models and are greatest in magnitude in the spike and regions of low collisionality. Increasing the Atwood number results in greater RT instability growth and reduced upward interface movement. Deviation of the distribution function from Maxwellian is inversely proportional to collision frequency and concentrated around the fluid interface. The linear phase of RT instability growth is well described by theoretical linear growth rates accounting for viscosity and diffusion.