Cynthia Riginos , Iva Popovic, Zoe Meziere, Vhon Oliver Garcia, Ilha Byrne, Samantha M Howitt, Hisatake Ishida, Kevin R Bairos-Novak, Adriana Humanes, Hugo Scharfenstein, Thomas J Richards, Ethan J Briggs, Vanessa Clark, Chuan Lei, Mariam Khan, Katharine E Prata

The conservation and management of coral reef ecosystems will benefit from accurate assessments of reef-building coral species diversity. However, the true diversity of corals may be obfuscated by cryptic yet genetically distinct groups, which are likely more pervasive than currently recognised. Here, we investigate the prevalence of cryptic coral groups and assess evidence for their permeability to gene flow (hybridisation) via a structured literature review of genomic studies. Using reproducible criteria to detect distinct genetic groups that are sympatric, we find that 68% of nominal species represented in population genomic studies show evidence for comprising partially reproductively isolated groups and that these distinct groups are often linked by gene flow. Cryptic genetic groups frequently segregate by environment, especially depth, and may differ by phenotypic characteristics including resilience to heat stress. This hidden biodiversity creates challenges for coral conservation and restoration planning that are not well appreciated, including hiding true population declines, biasing estimates for species’ phenotypic breadth, overestimating the resilience of species to stressors, yielding uncertainty in evolutionary dynamics inferred from past studies, and implying that reproductive barriers may limit mating between local and translocated corals. Incorporating the expectation that coral cryptic taxa with incomplete species boundaries will frequently be encountered is critical to the long-term success of coral conservation and restoration programs. Studying these phenomena in more detail will directly benefit conservation and restoration goals. Thus, we detail recommendations for best practice and strategies for identifying cryptic taxa and hybridisation. In addition, cryptic coral taxa present an untapped resource for studying speciation which could provide rich opportunities for collaboration among coral and speciation biologists and fill key knowledge gaps relevant to conservation and restoration.