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The data presented here support research article entitled ‘Trophic flexibility and prey selection of the wild long-snouted seahorse Hippocampus guttulatus Cuvier, 1829 in three coastal habitats’’ Ape et al., 2019. Determinations of the dietary composition, differences in prey selection and potential prey abundance and availability among three habitats at Taranto Mar Piccolo were based on the analysis of gut contents of seahorses and sediment samples. Both highly (Corallina elongata and Cladophora prolifera) and low complex (sandy bottom) habitats were investigated. Prey items were divided into two size classes: <1 mm and >1mm. Data about the total abundance of each prey size class in gut contents and sediments in three different habitats and PERMANOVA comparisons are given. Keywords: Hippocampus guttulatus, Gut content, Prey availability, Habitat type