Shallow coastal habitats represent some of the most valued ecosystems supporting complex communities of benthic organisms, delivering diverse ecosystem services. Cumulative activities of the benthic fauna affect the physical and chemical conditions of their environment and determine the rate of processes and benthic ecosystem functioning in coastal areas. However, excessive human use of the coastal zone puts extensive pressure on coastal ecosystems leading to biodiversity loss and habitat destruction. Therefore, it is essential to implement Ecosystem-Based Management (EBM) to ensure the protection of coastal resources whilst increasing the efficiency of their uses. Such EBM needs to be based on solid scientific evidence, including a detailed understanding of the link between biodiversity and ecosystem functioning.Macrofaunal assemblages have been shown to impact microbial-mediated nitrogen cycling processes in marine sediments through their role in affecting the physical and chemical conditions as they affect the exchange processes across the sediment-water interface. However, how the functional traits of macro-organisms, through the interactions with micro-organisms, affect microbial-mediated ecosystem functioning is still not fully understood. This PhD thesis aims to investigate the effect of macrofauna (at the community and species level) on benthic microbial communities (total bacterial and archaeal communities and specific functional groups, nitrifiers and denitrifiers) and the N-cycle processes mediated by them (nitrification and denitrification). The nitrogen cycle is one of the most important biogeochemical cycles in ecosystems. It provides nitrogen as an important component for all living cells and for primary production. It also counteracts eutrophication in the coastal marine area; it also releases back the biologically useful nitrogen into the atmosphere by converting it into gaseous compounds in both terrestrial and marine ecosystems (Canfield et al., 2005).