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The present study compared fish assemblages in two adjacent areas, one with drifting algae (A) and another without it (WA), in order to assess seasonal changes in diversity and composition. Both areas were located in Sao Cristovao beach, Rio Grande do Norte state, on the semi-arid North-Northeastern coast of Brazil. A total of 4988 individuals were caught, the most species-rich families being Scianidae, Ariidae, Engraulidae and Carangidae. Species richness and abundance were slightly higher in site A, but diversity and evenness were higher in site WA. However, with the exception of evenness, such differences were not significant at any time during the study. Species composition was also similar between the two sites over the year. Nevertheless, in spite of the similarities, seasonal changes of environmental conditions, particularly rainfall, seemed to influence fish assemblages differently in the two areas. This may have led to changes in assemblage structure, causing the differentiation of the communities in the dry season. The present study presents evidence that fish assemblages in habitats with and without drifting seaweeds are not static and may become more similar or different, depending on the environmental conditions, suggesting that there is a complex relationship between primary productivity, trophic level and the structure of fish assemblages.