The gorgonian Eunicella singularis (Esper, 1794) is abundant on rocky bottoms at Cap de Creus (42°18′49″ N; 003°19′23″ E) in the western Mediterranean, and this study compared zooxanthellate colonies from relatively shallow depths with azooxanthellate colonies living at depths to 60 m. The goal was to determine the taxonomic status of a previously described subspecies, E. singularis aphyta. Sampling at 10-m intervals from 20 to 60 m using scuba or a remotely operated vehicle (ROV) in 2004 and 2010 allowed examination of colony shape, sclerite variability, genetic variability, and the presence/absence of zooxanthellae. Two morphotypes were identified: a shallow morphotype with candelabra-like colonies at 20–30 m has zooxanthellae, while a deep morphotype with more ramified colonies at 40–60 m lacks symbionts. Sclerite differences among colonies were also identified along the depth gradient. The mitochondrial marker msh1 did not discriminate between the two morphotypes and indeed did not discriminate among several Mediterranean species of Eunicella. Other genetic markers will be needed to firmly establish the taxonomic status of the two depth-related morphotypes.