We investigate small scale equidistribution of random orthonormal bases of eigenfunctions (i.e. eigenbases) on a compact manifold M. Assume that the group of isometries acts transitively on M and the multiplicity of eigenfrequency tends to infinity at least logarithmically. We prove that, with respect to the natural probability measure on the space of eigenbases, almost surely a random eigenbasis is equidistributed at small scales; furthermore, the scales depend on the growth rate of multiplicity. In particular, this implies that almost surely random eigenbases on the n-dimensional sphere (n>=2) and the n-dimensional tori (n>=5) are equidistributed at polynomial scales.