Seagrass ecosystems have been declining, and restorations are conducted in many parts of the world to compensate for habitat loss and restore the ecosystem services seagrasses provide. Assessment of transplantation success requires the monitoring of the level of biodiversity between the donor and transplanted sites. In this study, we assessed a seagrass ecosystem after restoration in terms of the diversity of marine organisms using environmental DNA (eDNA) to compare four sites: (1) bare sand, (2) a natural meadow of Cymodocea serrulata, (3) a natural meadow of Halophila ovalis, and (4) a transplanted seagrass meadow. The results showed the presence of 3 domains, 34 phyla, 59 classes, 92 orders, 155 families, 156 genera, and 121 species. Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes were the dominant bacterial phyla. Among eukaryotes, Phragmoplastophyta/Charophyta (epiphytes), Ascomycota (fungi), Cnidaria (jelly fish), and Arthropoda (Crabs and bivalves) were the dominant phyla. Dugong tails and commercial species (sea cucumber, dog conch, and swimming crab) have been observed in both the natural and transplanted meadows. Relative abundance among the four sites was significantly different. There were no differences in species richness and evenness between the four sites and no differences in species richness and evenness between the natural meadows and the transplanted seagrass meadow. It is possible that transplanted seagrass meadow can be successfully restored and established and can provide habitat for fauna and microbes. Additionally, fauna are not limited in their capacity to move between the natural and transplanted habitats. This study provides an assessment of biodiversity of restored seagrass patches and a better understanding of a seagrass ecosystem after restoration. However, to assess seagrass ecosystem services after restoration and the success of restoration actions, long-term monitoring of marine organism diversity and additional assessments are needed.