The focus of this paper is to provide an overview of historical and modern accounts of scleractinian evolutionary relationships and classification. Scleractinian evolutionary relationships proposed in the 19th and the beginning of the 20th centuries were based mainly on skeletal data. More in-depth observations of the coral skeleton showed that the gross-morphology could be highly confusing. Profound differences in microstructural and microarchitectural characters of e.g., Mesozoic microsolenine, pachythecaliine, stylophylline, stylinine, and rhipidogyrine corals compared with nominotypic representatives of higher-rank units in which they were classified suggest their separate (?subordinal) taxonomic status. Recent application of molecular techniques resulted in hypotheses of evolutionary relationships that differed from traditional ones. The emergence of new and promising research methods such as high-resolution morphometrics, analysis of biochemical skeletal data, and refined microstructural observations may still increase resolution of the “skeletal” approach. Achieving a more reliable and comprehensive scheme of evolutionary relationships and classification framework for the Scleractinia will require close cooperation between coral biologists, ecologists, geologists, geochemists, and paleontologists.