Upwelling can determine important changes in community structure on rocky shores. However, studies on the meiofauna in areas of upwelling are scarce and do not include analysis on the species level for Copepoda Harpacticoida. The present study aimed to describe the Harpacticoida community in a region under the influence of coastal upwelling (Arraial do Cabo, Rio de Janeiro, Brazil). The hypothesis tested was that temporal differences in the fauna would be greater at the rocky shore more affected by upwelling. Samples were collected from the sublittoral of two rocky shores: Sonar, which is more exposed to upwelling, in January and June 2004; and Pedra Vermelha, which is a sheltered shore, in March and September 2002. Each sample consisted of four replicates collected by scraping epilithic algae along with the associated sediment. Weekly data on surface water temperature and nitrate content denoted stronger upwelling in 2002 compared to 2004. Nine genera of Copepoda Harpacticoida are reported for the first time for the Brazilian coast. Univariate indices identified no differences between rocky shores or seasons, whereas multivariate analysis indicated significant differences in assemblages between shores and between seasons. The strong variation in physicochemical conditions associated with upwelling favoured the dominance of opportunistic species, such as Parastenhelia spinosa. At the Sonar rocky shore, temporal differences were significantly stronger than at Pedra Vermelha, thereby confirming the initial hypothesis. These results indicated that the occurrence of upwelling had a very important role structuring the Harpacticoida assemblage at the species level.