We present a liner theory of the Rayleigh-Taylor instability in the equatorial ionosphere. For a purely exponential density profile, we find that no unstable eigenmode solutions exist. For a particular model ionosphere with an F peak, unstable eigenmode solutions exist only for sufficiently small horizontal wave numbers. In the later case, purely exponential growth at a rate identical to that for the sharp boundary instability is found. To clarify the situation in the case that eigenmodes do not exist, we solve the initial value problem for the linearized ion equation of motion in the long time asymptotic limit. Ion inertia and ion-neutral collisions are included. Assuming straight magnetic field lines, we find that when eigenmodes do not exist the growth of the response to an impulse is slower than exponential viz, t=-1/2 exp (&ggr;t) below the F peak and t-3/2 exp(&ggr;t) above the peak; and we determine &ggr;.