The composition of marine macroinvertebrates in two localities (Isla Palma and Los Negritos) of Malaga Bay was studied. This bay is located in the Pacific coast of Colombia and was recently declared National Natural Park. The rapid ecological assessment revealed a total of 128 species belonging to 64 families and 11 classes (including threatened species). The most common groups were: Gastropoda (27%), Polychaeta (26%), Malacostraca (16%) and Pelecypoda (13%). Even though the two sites are relatively near, being apart only by 6 km, the composition of the respective communities was very different. They shared only 7.8% of the species found; which might have profound and interesting effects for conservation purposes.