Protected Areas are established to protect significant ecosystems and historical artefacts. However, many are subject to little structured monitoring to assess whether the attributes for which they have been protected are being maintained or degraded. Monitoring sensitive areas using ground surveys risks causing damage to the values for which they are being protected, are usually based on limited sampling, and often convey insufficient detail for understanding ecosystem change. Therefore, there is a need to undertake quick and accurate vegetation surveys that are low impact, cost effective and repeatable with high precision. Here we use drone technology to map protected areas in Antarctica to ultra-high resolution and provide baseline data for future monitoring. Our methods can measure micro-scale changes, are less expensive than ground-based sampling and can be applied to any protected area where fine scale monitoring is desirable. Drone-based surveys should therefore become standard practice for protected areas in remote fragile environments.