The current centuries old classification of the family Nephtheidae is still mostly based on colony morphology. In this family the Indo-Pacifc genera Litophyton, Nephthea, Dendronephthya and Stereonephthya, and the Atlantic genus Neospongodes form a complex mix of closely related, poorly described species which cannot be recognized using only colony morphology. Attempts with the more modern approach of comparing skeleton composition (sclerites) have been only partly successful because of the extreme variation of sclerite forms present in these genera. The genus Chromonephthea Van Ofwegen, 2005, introduced for several species previously assigned to Dendronephthya, Nephthea and Stereonephthya, was established with sclerite morphology, but the true generic status of the majority of the nominal species of these genera remained unresolved. In an attempt to clarify the phylogenetic relationships between Litophyton, Nephthea, Stereonephthya and Chromonephthea fourteen specimens, unidentified but certainly belonging to these genera, have been used in molecular analyses. All analyses supported two clades, which could be related to the shape of the sclerites present in the polyp stalks. One clade contained the specimens with characters for Stereonephthya along with the Chromonephthea specimen as a sister group. The other clade had a ‘true’ Nephthea and Litophyton together with the specimens that could not be placed in any particular genus using the old classification criteria. The consequences of these results for nephtheid classification are discussed.