Highly productive and vulnerable habitats such as maerl and crinoid beds are subject to severe impacts from trawling in Mediterranean Sea. One of the most valuable target species that inhabit these habitats is the red mullet, Mullus barbatus, which can achieve there optimum feeding conditions based on infauna, which can provide some Fatty Acids (FAs) such as Polyunsaturated Fatty Acids (PUFAs) that are essential in shaping life history traits such as growth and reproduction. This study is the first one evaluating how habitat type can affect the FA profile of red mullet and that of their prey (infauna). The analysis was carried out in both habitats (maerl and crinoid beds) and compared to muddy bottom, the most common trawl fishing ground. In red mullet muscle from maerl or crinoid beds, we observed a higher concentration of PUFAs omega 3 and omega 6 such as C22:6n-3 (docosahexaenoic acid, DHA), C18:3n-3 (alfa-linolenic acid, ALA) or C18:2n-6 (linoleic acid) than in muddy bottoms. On the other hand, MUFAs such as C18:1cn-9 (oleic acid) presented higher concentrations in muddy bottoms compared to maerl habitat. Regarding infauna's FAs, there was between 30% and 35% of dissimilarity between maerl and crinoid habitats and muddy habitat respectively. In addition, differences found in infauna's PUFAs concentration were very similar to the differences found in M. barbatus PUFAs when maerl and crinoid were compared with muddy habitats. Our results support the idea of using FAs as an indicator of the quality and trophic marker of productive and sensitive benthic habitats, which can contribute to assess the good environmental status (GES) of these habitats and the goods and services they provide.