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Meiofauna in sediments colonized by Posidonia oceanica in the Ligurian Sea (NW Mediterranean) was investigated to evaluate its use as an early warning indicator of environmental disturbance. Descriptors commonly used in seagrass health assessment are mainly related to the plant (e.g., phenological parameters) and/or to the meadow (e.g., structural parameters) and are subjected to long-term response times. Conversely, meiofauna is considered a good bioindicator with a rapid response to environmental variations, due to its main features (e.g., short life cycle, scarce mobility, presence/absence of tolerant/sensitive species). Meiofaunal community, sediment characteristics and organic matter descriptors in three meadows located in urbanized coastal areas were contrasted with those observed in three meadows located within Marine Protected Areas. Samplings were carried out in two distinct periods, at the beginning and at the end of the summer season, in order to individuate early changes in the meiofaunal assemblages. The meiofauna and, particularly, the nematode assemblage composition and diversity, highlighted differences among meadows at the end of the summer not detectable by organic matter descriptors and structural parameters of the meadow (e.g. shoot density). Nematodes are, thus, proposed as appropriate biological quality elements (BQEs) able to show early responses to environmental disturbance.