Coral reefs have high biodiversity and are important as ecosystem engineers, providing microhabitats for a large number of organisms. This study examines the patterns of diversity, abundance and structure of gorgonian epifaunal communities found in Ecuador, a well-recognized marine biodiversity hot spot. Within this area, Leptogorgia manabiensis and L. obscura represent two of the most abundant and widely distributed gorgonian species, each with differing morphological characteristics. Epifaunal communities associated with these host species were analyzed during both the cold (June) and warm (November) seasons over two consecutive years. Both species were shown to be highly effective benthic biodiversity ecosystem engineers, hosting denser communities than other related organisms such as scleractinians, other gorgonians, algae, sponges, hydrocorals and bryozoans, as well as other geographic areas. A complex pattern of biodiversity was observed, with each gorgonian species hosting distinct communities: The fan-shaped L. manabiensis had a less diverse community dominated by echinoderms (mainly ophiuroids), while the bush-shaped L. obscura was dominated by crustaceans (mainly amphipods). Although the morphology of L. obscura allowed for greater living space for associated fauna, this species exhibited a less dense epifaunal community than of L. manabiensis. A seasonal fluctuation in abundance was also observed. Abundance tended to be greater in the cold season (June), likely due to the influence of the cold, nutrient-rich Humboldt Current, than in the warm season (November), when the warm, nutrient-poor Panama Current dominates. Diversity was not affected by seasonal fluctuations and remained constant throughout the year.