The Ile du Grand Connétable nature reserve is a rocky island off the Northern Atlantic coast of South America that hosts a unique population of Magnificent Frigatebirds (Fregata magnificens, Pelecaniformes). A high chick mortality, associated with nodular proliferative lesions, involving featherless areas, such as legs, neck, eyelids, and beak, was recorded during a consecutive 2 yr and affected almost half of the generation. Investigations were, therefore, conducted to determine the cause of these epidemics. Although histopathologic investigations suggested that malnutrition, because of fewer resources in the Frigates’ fishing area, could be the cause of the epidemic, a novel alphaherpesvirus, tentatively called Fregata magnificens herpesvirus, was detected in cutaneous crusts on the diseased birds. Although in this study, we do not prove the causal link of this new virus to the symptoms observed, it can nevertheless be suggested that in debilitated hosts, a productive herpesvirus infection might accelerate, and/or be accelerated by, population declines. These results emphasize the need to take into consideration the possible role of herpesviruses in weakened populations of wild birds in conservation management plans.