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The present study is aimed at implementing the amplicon sequence variant (ASV) concept to describe meiofaunal species composition independent of morphological identification, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify an 18S barcode from a variety of meiofaunal taxa, compatible with the high throughput sequencing (HTS) Illumina 300 X 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 contigs. Five quality scores (q=35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs to the DADA2 software, ending with 5 reference ASV libraries. Each of them was clustered, applying 3% dissimilarity threshold and revealed an average number of 1.38±0.078 ASVs/cluster which demonstrate high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs/3% cluster, strongly indicate compatibility with the actual number of underlying species. Hence, the q=25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342 - 3% clusters with average number of 1.34±1.036 ASV/cluster and their BLASTN annotation elucidated the expected meiofaunal taxa. The 16 assemblies of sample-specific paired contigs were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and also normalized to the actual number of individuals in each sample.