This course provides attendees with: 1) a complete review on the current status of coral reef and seagrass remote sensing, 2) a step-by-step procedure to collect field data to be used for image-based mapping in both benthic environments, and 3) an introduction to the mathematics needed for optimization of MPA networks, and an example of how to use maps to design such networks. Many practical and useful examples from case studies are included throughout.