Recent molecular analyses have challenged many traditional notions concerning the systematics and evolution of scleractinian corals. Phylogenetic analyses of mitochondrial and nuclear genes have shown that several traditional families are polyphyletic (e.g, Faviidae, Mussidae), as are many genera that are conventionally assigned to them (e.g., Montastraea, Favia, Scolymia). The analyses reveal a previously-unrecognized clade, which consists exclusively of Atlantic members of the families Faviidae and Mussidae. The results argue against the close evolutionary relationships that have long been assumed between Atlantic and Pacific corals, and indicate that divergence pre-dated final closure of the Central American Isthmus in the Pliocene and occurred perhaps as early as Eocene. The results call into question morphological characters that have traditionally been used in scleractinian classification, and indicate that new characters that reflect skeletal growth need to be found to serve as phylogenetic markers. Discovery of such characters is critical for tracing the evolutionary history of scleractinians in the fossil record.

As an example, a comprehensive survey of skeletal morphology is conducted in the family Mussidae; focusing on four Atlantic genera (Isophyllia, Mussa, Mussismilia, Mycetophyllia), four Indo-Pacific genera (Acanthastrea, Lobophyllia, Symphyllia, Cynarina), and one cosmopolitan genus (Scolymia). Three different groups of characters were compared among molecular clades: (1) traditional macromorphology (colony formation, budding, and the size and shape of corallites) using regular light microscopy, (2) micromorphology (septal teeth, ornamentation) using scanning electron microscopy (SEM) of calical surfaces, and (3) microstructure (fibers, calcification centers) using transverse thin sections and SEM of polished and etched sections. Although most macromorphologic characters exhibit homoplasy, differences between Atlantic and Pacific mussids are observed in the shape and differentiation of septal teeth, septal ornamentation, and thickening deposits associated with the septa and wall. These observations together with similarities between Atlantic mussids and faviids support the molecular results, which suggest an Eocene divergence.