Autonomous underwater vehicles (AUVs) are increasingly being used to collect physical, chemical, and biological information in the marine environment. Recent efforts have been made to merge AUV technology with acoustic telemetry to provide information on the distribution and movements of marine fish. During 2010, we conducted a study in coastal waters near Juneau, Alaska to determine the feasibility of using AUVs to locate marine species under rigorous field conditions, and to compare this approach with traditional vessel-based tracking. Tracking surveys were conducted with a REMUS 100 AUV equipped with an integrated acoustic receiver and hydrophone. The AUV was programmed to navigate along predetermined routes to detect acoustic transmitters within the area. Comparable surveys were conducted with a boat equipped with acoustic tracking gear. Moorings with transmitters at 20-500 m were deployed to provide acoustic targets at known locations and depths. Marine fishes and crabs were tagged to provide mobile targets. Transmitter depth had a major impact on tracking performance. The AUV was equally effective or better detecting reference transmitters in shallow water, and significantly better than the boat for transmitters at deeper depths. Similar results were observed for the tagged animals. Crabs at moderate depths were recorded by both tracking methods, while only the AUV detected fish at depths exceeding 500 m. The AUV periodically had difficulty navigating and maintaining course due to the strong currents and extreme depths in the area. AUVs with greater cruising speeds, increased operating depths, and improved navigation would enhance AUV performance in marine environments.