The scleractinian coral Cyphastrea is a common and widespread genus throughout the coral reefs of the Indo-Pacific. Little is known about the phylogenetic relationships within this taxon and species identification is based mainly on traditional skeletal characters, such as the number of septa, septa cycles, growth form and corallite dimensions. Here we present the first focussed reconstruction of phylogenetic relationships among Cyphastrea species, analysing 57 colonies from the Red Sea, where five morphospecies live in sympatry. Analyses based on three loci (nuclear histone H3, 28S rDNA and a mitochondrial intergenic region) reveal the existence of three well-supported molecular lineages. None of the five previously defined morphospecies are monophyletic and they cluster into two clades, suggesting the need of a systematic revision in Cyphastrea. The third lineage is described as C. magna Benzoni & Arrigoni, sp. nov., a new reef coral species collected from the northern and central Red Sea. Cyphastrea magna Benzoni & Arrigoni, sp. nov. is characterised by the largest corallite diameter among known Cyphastrea species, a wide trabecular columella >1/4 of calice width, and 12 equal primary septa. This study suggests that morphology-based taxonomy in Cyphastrea may not identify monophyletic units and strengthens the application of genetics in coral systematics.