Once common along the Gulf of Mexico coast, the endangered West Indian manatee (Trichechus manatus) is now most abundant in peninsular Florida. In recent years, there has been a greater number of manatee sightings in areas west of Florida, suggesting increased use of habitats in the northern Gulf of Mexico (nGOM). To define manatee movement patterns and habitat use in Alabama waters and clarify relationships between apex populations and animals that visit the nGOM, our research coupled empirical sighting and habitat data with remotely sensed and biochemical data. Specifically, we analyzed data from a) satellite and telemetry-based tagging and monitoring (via satellite/GPS, radio telemetry, handheld hydrophone, visual observation, and passive acoustic monitors) of manatees tagged in Alabama waters, and b) stable isotope and trace element analyses of tissues and ear bones from manatees that died in Alabama and Mississippi waters in the past 6 years. This collaborative research has provided groundbreaking evidence of the importance of Alabama habitat to some Florida manatees, shown by site fidelity and diverse demographics of seasonal manatee populations, and shifts in diet related to long distance seasonal migration patterns. Over time, these data will refine current understanding of the spatial and temporal boundaries of manatee habitat and inform understanding of animal movements in response to environmental change. Outputs will be useful to guide management and conservation programs by providing baseline data for assessment of environmental perturbations (habitat loss, severe storms, oil spills, climate change) on distribution and movements of manatee and other migratory species throughout their range.