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Background  In recent years, several types of molecular markers and new microscale skeletal characters have shown potential as powerful tools for phylogenetic reconstructions and higher-level taxonomy of scleractinian corals. Nonetheless, discrimination of closely related taxa is still highly controversial in scleractinian coral research. Here we used newly sequenced complete mitochondrial genomes and 30 microsatellites to define the genetic divergence between two closely related azooxanthellate taxa of the family Caryophylliidae: solitary  Desmophyllum dianthus  and colonial  Lophelia pertusa .    Results  In the mitochondrial control region, an astonishing 99.8 % of nucleotides between  L. pertusa  and  D. dianthus  were identical. Variability of the mitochondrial genomes of the two species is represented by only 12 non-synonymous out of 19 total nucleotide substitutions. Microsatellite sequence (37 loci) analysis of  L. pertusa  and  D. dianthus  showed genetic similarity is about 97 %. Our results also indicated that  L. pertusa  and  D. dianthus  show high skeletal plasticity in corallum shape and similarity in skeletal ontogeny, micromorphological (septal and wall granulations) and microstructural characters (arrangement of rapid accretion deposits, thickening deposits).    Conclusions  Molecularly and morphologically, the solitary  Desmophyllum  and the dendroid  Lophelia  appear to be significantly more similar to each other than other unambiguous coral genera analysed to date. This consequently leads to ascribe both taxa under the generic name  Desmophyllum  (priority by date of publication). Findings of this study demonstrate that coloniality may not be a robust taxonomic character in scleractinian corals.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0654-8) contains supplementary material, which is available to authorized users.

Merging scleractinian genera: the overwhelming genetic similarity between solitary Desmophyllum and colonial Lophelia