Marine protected areas (MPAs) are a powerful tool for conserving marine biodiversity when designed using ecological information and conservation goals and targets. Dugongs (Dugong dugon) were not an explicit target in the design of the network of MPAs in New Caledonia, despite being one of the region’s World Heritage values. Our study retrospectively assessed the capacity of the New Caledonia MPA network to protect dugongs from anthropogenic threats. We developed a spatially explicit model of dugong distribution and relative density based on information collected from ∼10 years of aerial surveys. We quantified the amount of overlap between areas supporting high densities of dugongs and MPAs. We found that most of the important dugong habitats of New Caledonia had a low coverage of MPAs that provide high levels of restriction on anthropogenic activities. We identified several important dugong habitats along the west and the north-east coast that were not covered by MPAs and should be a priority for future management. The spatial mismatch between MPAs and dugongs was likely caused by weaknesses in the planning process, including the: (1) lack of explicit conservation goals and targets; (2) omission of spatial information on species’ distribution; (3) mismatch of spatial scales; (4) cost considerations; and (5) incorrect application of the IUCN protected area categories. We provide guidance on how these shortcomings can be avoided for marine species of conservation concern in New Caledonia and other regions.