Despite extensive studies on the taxonomy of fossil otoliths, the diversity of late Quaternary to Recent sea bottom otolith assemblages remains largely unexplored. Otolith assemblages from bottom sediments of the North-eastern Atlantic (NE Atlantic), central Mediterranean, and Red Sea were described based on a dataset of 9696 identifiable otoliths. Diversity estimators were computed and taxonomic compositions were compared against geographical site and depth gradient. Several species from the Red Sea show previously unnoticed range extensions or ancient occurrences, suggesting that the otolith assemblage requires further exploration in this region. The diversity is high in the NE Atlantic and central Mediterranean, whereas Red Sea assemblages are dominated by few taxa. We find that, departing from Modern fish communities, the richness of otolith taxa peaks at mid-water depths (500–1500m) and decreases at depths >2000m. The lower diversity at shallow water suggests environments not favorable for otolith preservation. The assemblages are geographically distinct, due to unique combinations of mesopelagic taxa specific to each sample area, though areas in the central Mediterranean and middle-latitude NE Atlantic share many taxa. Depth does not seem to structure otolith assemblages in the central Mediterranean because the otolith composition in this region is highly variable at depths <500m but poorly variable at greater depths. The discrepancies between otolith thanatocoenoses and fossil assemblages and the potential application for reconstructing ancient fish communities are discussed. Illustrating otoliths that are rarely found in the literature, this study is the first descriptive and comparative diversity analysis on Recent otolith assemblages for the regions of interest.