The majority of biochemical studies in corals has been focused on the lipidic composition and little attention has been given to the amino acid profile of these invertebrates. The objectives of this work were to investigate, for the first time, the temporal variations in the total amino acid (AA) composition of an octocoral, namely the sea pen Veretillum cynomorium, and to evaluate possible interspecific differences in AA profile between this octocoral and hexacorals. The quantitatively most important AAs in V. cynomorium colonies were: glutamic acid, varying from 3.92 to 5.94% dry weight (dw) and representing around 14–15% of total AA content; aspartic acid (3.34–4.99% dw; 11–12%); and glycine (2.87–4.57% dw; 9–12%). On the other hand, the minor AAs were methionine (0.41–0.73% dw; 1–2%) and histidine (0.54–0.76% dw; 2%). Almost all AAs showed the same significant seasonal variations, with the highest values in February, second highest in October and the lowest in June. Some AAs, namely lysine, phenylalanine and methionine did not follow this trend and showed the major peak in October. Most of the AA variations seemed to be linked to changes in food availability and/or gametogenesis. Principal component analysis clearly separated the octocoral from the group of hexacorals, mainly due to the higher percentages of arginine, tyrosine and glycine in V. cynomorium, and valine, serine, histidine, isoleucine and alanine in hexacorallia species. We speculate that this differentiation possibly derived from physiological differences related to phylogeny, and was not affected by reproductive or environmental seasonality.