This paper presents a method for the automatic creation of 2D mosaics of the sea floor, using video sequences acquired at different altitudes above the sea floor. The benefit of using different altitude sequences comes from the fact that higher altitude sequences can be used to guide the motion estimation of the lower ones, thus increasing the robustness and efficiency of the mosaicing process. When compared to the case of single sequence mosaic creation, we show that by combining geometric information from different sequences, we are able to successfully estimate the registration topology of much lower altitude sequences. This results in higher resolution mapping of the sea floor. Illustrative results are presented using sequences of the same coral reef patch, captured with a single video camera. The sequences present some of the common difficulties of underwater 2D mosaicing, namely non-flat, moving environment and changing lighting conditions. The importance of this work is emphasized by fact that the presented methods require inexpensive image acquisition and processing equipment, thus potentially benefiting a very large group of marine scientists.