Repeatable and accurate seagrass mapping is required for understanding seagrass ecology and supporting management decisions. For shallow (20 m). Here, we demonstrate and evaluate the use and potential advantages of AUV field data collection for calibration and validation of seagrass habitat mapping of shallow waters (2), Moreton Bay, Australia. In the field, georeferenced photographs of the seagrass were collected along transects via snorkelling or an AUV. Photographs from both collection methods were analysed manually for seagrass species composition and then used as calibration and validation data to map seagrass using an established semi-automated object-based mapping routine. A comparison of the relative advantages and disadvantages of AUV and snorkeller-collected field data-sets and their influence on the mapping routine was conducted. AUV data collection was more consistent, repeatable and safer in comparison with snorkeller transects. Inclusion of deeper water AUV data resulted in mapping of a larger extent of seagrass (~7 km2, 5% of study area) in the deeper waters of the site. Although overall map accuracies did not differ considerably, inclusion of the AUV data from deeper water transects corrected errors in seagrass mapped at depths to 5 m, but where the bottom is visible on satellite imagery. Our results demonstrate that further development of AUV technology is justified for the monitoring of seagrass habitats in ongoing management programmes.