The genus Eunicea is the most abundant and diverse group of Octocorals in Caribbean reefs with more than 30 species described, however, only 16 of them are considered valid until now, underestimating the real diversity in this group. In this study, we provide a phylogenomics approach with nextRAD sequencing, a reduced-representation sequencing coupled to Illumina technology, to scan thousands of SNP across the genome over more than 200 Eunicea samples, from different species, across the Caribbean.