Marine infrastructure can selectively favour the spread of non-indigenous marine organisms (NIS) in biofouling that often leads to severe environmental and economic damage. Post-border detection methods rely almost exclusively on morpho-taxonomy but are limited for cryptic organisms or larvae. Molecular genetic tools promise greater detection sensitivity. However, limitations such as molecular marker choices or incomplete databases still need to be overcome. This study combined conventional morpho-taxonomy, 18S rRNA and COI metabarcoding approaches for most reliable NIS detections on settlement plates.