Pipefish are a vulnerable and diverse group of ichthyofauna tightly associated to seagrass meadows, key habitats in shallow marine areas. Despite of their charismatic role, main ecological features, habitat and diet of this group remain largely unknown. This study focuses on assessing pipefish habitat and feeding preferences including different hosting seagrasses such as Posidonia oceanica and Cymodocea nodosa from the Balearic Islands, western Mediterranean. Four species (Syngnathus typhle, S. abaster, Nerophis ophidion and N. maculatus) were found associated to different seagrasses. S. typhle and N. maculatus were more frequent in P. oceanica meadows, while S. abaster and N. ophidion in C. nodosa. Individuals of all species captured in P. oceanica were larger than those living in C. nodosa, suggesting a size-dependent habitat preference. Feeding preferences, however, were driven by prey availability and fish features, e.g head/snout morphology. For the first time in the western Mediterranean, a thorough description of the diet and potential preys of this group was carried out. Epifaunal assemblages (potential prey) were dominated in both habitats by harpacticoid copepods and gammarid amphipods, and they were also the primary preys according to stomach contents of all species. These results can contribute to future pipefish conservation and management actions, such as targeting crucial habitat identification and designing culture and reintroduction protocols.