Owing to technical problems and difficult taxonomic identification, meiofauna have been generally less studied than macrofauna. However, the role of meiofauna in marine ecosystem functioning, and their effective and rapid response to anthropogenic alterations and climatic changes have recently been acknowledged, leading to increasing scientific and applied interest. At present, systematic and biogeographic knowledge of the meiofauna of the Adriatic Sea is extremely heterogeneous, because most of the data are limited to a few taxa and the sampled areas are scattered, being located mainly in the coastal areas of the northern basin. Analysis of the composition and distribution of meiobenthic groups in the Adriatic Sea highlights the presence of several endemisms. Meiofauna also include bioindicator taxa, which allow assessment of the quality of marine sediments; this is particularly useful in systems characterised by the synergistic effect of different forms of anthropogenic impact, such as the Adriatic basin. Current knowledge about the ecology of the meiofauna and use of this component in applied ecological studies, along with the availability of a standardised protocol for the analysis of meiofaunal assemblages, allows us to recommend formal acknowledgement of the need to integrate information derived from the analysis of macrofauna with information derived from the study of meiofauna. Future research based on the simultaneous use of both of these benthic components will allow faster and more accurate evaluation of the response of coastal marine ecosystems to anthropogenic disturbance.