COI and 18S reference databases, taxonomic assignments of Amplicon Sequence Variants, as well as all scripts used in the project -Metabarcoding meiofauna biodiversity assessment in four beaches of Northern Colombia: Effects of sampling protocols and primer choice- ABSTRACT Environmental DNA (eDNA) metabarcoding can enhance understanding of global biodiversity by making it possible to study taxonomic groups that are difficult to sample. However, experimental choices made when generating eDNA data can impact biodiversity surveys, and must be carefully considered during study design. Here, we explored the impact of DNA extraction protocol and metabarcode choice on recovery of meiofauna DNA from sand. We extracted DNA from untreated sand and from sand treated with either Ludox or MgCl2, and amplified DNA using the 18S and CO1 metabarcodes. We found differences in species composition and richness both between metabarcodes and among sampling strategies, confirming the sensitivity of the experiments to both parameters. Combining data from multiple barcodes and from multiple extraction protocols increased recovered meiofaunal taxonomic diversity. Future metabarcoding studies and meta-analyses should consider the effects of sampling protocols on biodiversity. Our results also highlight the need to continue to improve existing reference databases of morphological and molecular characterization of meiofauna, in particular of the tropics, which are poorly represented in existing databases.