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Marine underwater habitats dominated by seagrass Posidonia oceanica play an essential role in fish community assembly, affecting taxonomic and functional diversity, abundance and fish behavior. The value of seagrasses as habitat depends on the spatial arrangement of the seascape elements and the availability of alternative habitats. Little is known about the effect of the seascape context of P. oceanica meadows on fish assemblages in the Mediterranean Sea. To identify P. oceanica meadows’ relative importance as a habitat for fishes, fish communities in the Croatian Adriatic Sea were investigated, using SCUBA lure-assisted visual census. The results show a significant effect of different arrangements of P. oceanica meadows’ seascape elements and surrounding habitats on fish community structure. Fragmented mosaic meadows with P. oceanica growing directly on and between rocky-algal reefs/boulders had significantly higher fish abundances compared to both types of continuous meadows (bordering rock and bordering sand). Continuous meadows bordering sand harbored the highest number of unique species. Evidence that alternative structured habitats within proximity to seagrass beds may affect the community structure of associated fish assemblages is provided, highlighting the need to consider P. oceanica meadows’ seascape context in conservation management and experimental design for fish community structure.