ABSTRACTNeogoniolithon is a widespread genus of non‐geniculate coralline algae in the Mediterranean Sea. Three vaguely differentiated species have been reported in the region. This study examined the diversity of Neogoniolithon in the Mediterranean by inferring phylogenies using psbA and COI‐5P markers, applying delimitation algorithms and comparing morpho‐anatomies of putative species. In contrast to previous reports, 13 species were delimited from the Mediterranean in two distant clades. Initial observations suggested that tetrasporangial conceptacle size might be used to separate the two clades. Only three species showed fruticose morphologies. Further morpho‐anatomical differentiation was difficult. One species included Mediterranean, Pacific and Atlantic samples, while three other species occurred in the Mediterranean and the Canary Islands. The global tree revealed that most species were geographically restricted. Crypticity in multiple lineages implied a much higher diversity than currently reported, even lacking samples from the eastern Mediterranean. Only sequence data can be used to identify these cryptic lineages. High endemism emphasizes the importance of conservation of coralline algal bioconstructions to prevent extinctions. The presence of cryptic diversity also invites a reassessment of the knowledge on species distributions that are important in conservation planning and management.