Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (ASLs), has become one of the busiest countries in the world with varied shipping activities. These actions have the ability to facilitate the transmission of species (bio-invasion). Until recently, the number of global introduced species has increased, with negative consequences for environment and the economy. Environmental DNA (eDNA) approaches for detecting the presence of invasive species are currently receiving a lot of interest as a broad approach method in ecological research. As a result, the study used the eDNA technique to compare the quantity and variety of introduced species from the Cnidaria and Porifera Phyla, as well as to characterize their invasiveness status and possible presence in the waters of Jakarta Bay. Based on data from the inside Zone of National Park (ZI) and Outside Zone of National Park (ZO), the biological community composition, richness, and diversity were assessed (ZO). The mBrave workflow generated a total of 14,275 reads from high-throughput sequencing of amplicons from two zones, with 8,917 reads in ZI and 5,358 reads in ZO. Blackfordia virginica , Cordylophora caspia , and Ectopleura crocea were among the imported species included in the invasive category, with E. crocea having the highest abundance and being detected in both zones, with a total of 1300 reads, consisting of 1253 reads in ZI and 47 reads in ZO. Based on the findings, the eDNA methodology can be used as a biomonitoring and conservation method for invasive species.