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This paper presents a robust algorithm for the registration of airborne video sequences with reference images from a different source (airborne or satellite), based on phase-correlation. Phase-correlations using Fourier-Melin Invariant (FMI) descriptors allow to retrieve the rigid transformation parameters in a fast and non-iterative way. The robustness to multi-sources images is improved by an enhanced image representation based on the gradient norm and the extrapolation of registration parameters between frames by motion estimation. A phase-correlation score, indicator of the registration quality, is introduced to regulate between motion estimation only and frame-toreference image registration. Our Robust Phase-Correlation registration algorithm using Motion Estimation (RPCME) is compared with state-of-the-art Mutual Information (MI) algorithm on two different airborne videos. RPCME algorithm registered most of the frames accurately, retrieving much better orientation than MI. Our algorithm shows robustness and good accuracy to multisource images with the advantage of being a direct (non-iterative) method.