Research on the habitats protected by the European Union's Habitats Directive (HD) has increased rapidly since its adoption in 1992. However, the methods and tools used to assess their conservation status are varied. In this context, we reviewed and summarized the scientific literature related to the coastal Natura 2000 habitats to list and sort parameters used to assess and map their conservation status. We found 225 papers that specifically focused on the assessment of conservation status of coastal habitats. An analysis of the papers was conducted based on the four parameters (“Range”, “Area”, “structure and functions”, “Future prospects”) specified in the guidelines. Results highlight knowledge gaps regarding the availability of data and methods that measure the “Range”, “Area”, “Structure and functions” and “Future prospects”. Most of the papers focused on coastal dunes and were located in the Mediterranean biogeographic region. Therefore, the process of assessing the conservation status of coastal habitats remains complicated to implement because methodological approaches are mainly dominated by expert statements. Moreover, all the procedures of the HD are carried out within each member country and the final assessments are often the synthesis of these partial assessments. However, the multiscalar approach and the use of innovative technologies (databases, remote sensing) can be particularly relevant to develop replicable approaches and facilitate monitoring and the implementation of management measures. •The implementation of HD remains complicated today to assess and monitor the conservation status.•Methodological disparities exist between coastal habitats, between countries and between biogeographic regions.•Currently, methodological approaches remain mainly based on expert judgements.•Recent and innovative methods for automatic and objective modelling can help to assess habitat range and area.•Concerted and multiscalar approaches can help to improve knowledge on structure, functions and future prospects.