Ports and marinas are global hotspots for non-indigenous species (NIS), yet biofouling communities in the Arabian Gulf remain poorly documented. Here, we present the first spatially extensive assessment of biofouling communities along ~ 300 km of the Saudi Arabian Gulf coastline. Across 12 sites, we combined COI metabarcoding of scrapings from pontoons/docks and settlement panels with image-based analysis of same panels to characterize taxonomic composition and quantify native, cryptogenic, and non-indigenous taxa. Community analyses revealed a clear site-level differentiation across all datasets, while broader geographic locations and environmental risk categories explained little variation. DNA metabarcoding detected more taxa than visual analyses, including 57 cryptogenic and NIS, many of which could not be visually detected. Industrial and commercial ports harbored higher NIS richness and relative abundance than recreational marinas, indicating localized invasion risk. Despite the sensitivity of DNA-based approaches, species-level assignments must be interpreted cautiously due to sparse regional reference libraries and limited representation of Gulf taxa in global databases. By generating one of the first spatially explicit baselines of biofouling biodiversity and NIS in the northwestern Indian Ocean, our study underscores the urgent need to expand region-specific reference databases and to implement integrated, site-resolved monitoring frameworks to support emerging marine biosecurity programs across this understudied system.