The evolutionary history of the Caribbean candelabrum octocorals from the genus Eunicea (Plexauridae: Octocorallia) remains unknown despite their high diversity and abundance in reef environments. Understanding the evolutionary relationships between and within the Eunicea species is critical to accurately measuring the group diversity. Furthermore, this group has a high potential for cryptic diversity and new species, particularly given the rich morphological variability. Conventional molecular markers, however, have not provided a precise positioning for the species inside the genus. Here, we provide the first phylogenomic reconstruction of these candelabrum octocorals employing NextRAD, a reduced-representation sequencing technique, to generate thousands of SNPs. We include 15 morphospecies sampled between valid and new species throughout the Caribbean. At large, the phylogeny is well supported and resolved. In total, 13 species-level clades are discernible, including two lineages with demonstrated genetic and morphological variation that are considered and described as two new species, Eunicea criptica sp. nov. and E. colombiensis sp. nov., both previously assigned as E. clavigera and the second as the “thick morphotype”, thereby increasing the diversity of the group. Understanding the magnitude of species diversity within Eunicea is essential for directing conservation initiatives and clarifying the biological processes in reef ecosystems.