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The <3% dissimilar Amplicon Sequence Variant (ASV) clusters of the 18S‐V4 barcode were used as species‐proxies for the evaluation of ASV composition and ASV diversity indices characterizing the hitherto poorly investigated meiofaunal communities of the south‐eastern part of the Levantine basin. Accompanied by abundance measurements, the relationships of these characteristics with sedimentary and bottom terrain parameters were interpreted. The construction of community composition profiles, namely ASVs' list and their estimated abundances, was done using our previously established procedure (Harbuzov et al., 2022, Marine Genomics 65, 100980), combining metabarcoding with sample reads normalization by the abundance of hard‐bodied meiofaunal taxa. The study province included the 54–1418 m depth range, across vertical sub‐bottom horizons ranging 0–17 cm. Oxygen, hydrogen sulfide and methane concentrations in the pore water, as well as sediment grain size spectra and sedimentary protein and carbohydrate levels, were measured, followed by an evaluation of their involvement in the shaping of the meiofaunal communities' characteristics. Community composition was generally site‐and‐horizon dependent and its abundance decreased with increasing bottom depth and across sub‐bottom horizons, typical to benthic habitats which are nourished by organic carbon from the euphotic zone. The relatively sharply inclined continental slope bottom located in the northern part of the Israeli coast was an exception. Its meiofaunal community characteristics were speculated to be affected by intensive sediment mixing and lateral transport of food from the shelf, in addition to the effect of the euphotic zone‐originated food sources. [ABSTRACT FROM AUTHOR]