International audienceAn analysis of low order mode coupling equations is used to describe the nonlinear behaviour of the Rayleigh-Taylor (RT) instability in the equatorial ionosphere. The nonlinear evolution of RT instability leads to the development of shear flow. It is found that there is an interplay between the nonlinearity and the shear flow which compete with each other and saturate the RT mode, both in the collisionless and collisional regime. However, the nonlinearly saturated state, normally known as vortices or bubbles, may not be stable. Under certain condition these bubbles are shown to be unstable to short scale secondary instabilities that are driven by the large gradients which develop within these structures. Some understanding of the role of collisional nonlinearity in the shear flow generations is also discussed