Marine caves constitute vulnerable habitats with unique and diverse biocoenoses. Monitoring these habitats is still challenging, which hinders the ability to evaluate global and local pressures that threatens their ecological value. In this study, ecological quality is estimated in twenty-one marine caves distributed along the northern and southern coasts of the Alboran Sea, a highly understudied area regarding marine caves. For that purpose, adjustments on the original Cave Ecosystem Based Quality Index (CavEBQI) are suggested in order to efficiently estimate the ecological quality of marine caves. Several methodological aspects regarding the assessment of biotic coverage, the visual census of motile fauna and the plasticity of the index usability were evaluated. Ecological quality of marine caves was in average “good” although it ranged between “poor”, “moderate” and “good” depending on the features of each cave. This study emphasizes the importance of adapting biotic indicators to biogeographical differences and technological advancements.