Marine migratory species tend to be overlooked in marine spatial planning due to limited knowledge of their habitats and migration pathways, resulting in a disconnect between animal migration ecology and spatial management decision making. The aim of this study was to predict the migratory corridors, suitable habitats and use of marine reserves by pygmy blue whales and overlap with marine traffic. Firstly, based on available telemetry data, we analysed the home ranges, core-use areas and migratory corridors using Brownian Bridge Movement Models. Secondly, we predicted suitable habitat by modelling telemetry data against environmental predictors using Maximum Entropy modelling; and lastly we geometrically overlaid home ranges and suitable habitats with designated migration lanes, marine protected areas and marine traffic. Consistent movement of pygmy blue whales from Western Australia to the Banda and Molucca Seas in Indonesia demonstrated a high level of connectivity between the two regions. There is a discrepancy between the designated migration lanes for large whales in Indonesian marine spatial planning and migration routes suggested by this study. The home range analysis and habitat models revealed that large areas of the migration corridors, core-use, and suitable habitats are currently not protected, particularly along international waters and within the Banda and Molucca Seas. The results can aid marine conservation planning by delineating the important areas and areas with high marine traffic density to optimise migratory species protection.