Caves with dim natural light, and lighted hypogean environments, have been found to host phototrophic microorganisms from varioustaxonomic groups. These microorganisms group themselves into assemblies known as communities or biofilms, which are associated withrock surfaces. In this work, the phototrophic biofilms that colonise speleothems, walls and floors in three tourist caves (Spain) were studied.Confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) were used to study these organisms and acquirethree-dimensional data on their biofilm structure. CLSM was used in a multi-channel mode whereby the different channels map individualbiofilm components. Cyanobacteria, green microalgae, diatoms, mosses and lichens were found to be grouped as biofilms that differedaccording to the sampling sites. The biofilms were classified into six types regarding their environmental conditions. These types weredefined by their constituent organisms, the thickness of their photosynthetic layers and their structure. Light-related stress is associated with lower biofilm thickness and species diversity, as is low humidity, and, in the case of artificially illuminated areas, the duration of lightexposure.