Abstract: Cetaceans are the top predators in marine ecosystems and play a crucial role in maintaining the stability and balance of marine food webs. The Beibu Gulf is an important fishing ground in the northern part of the South China Sea, characterized by rich fishery resources and biodiversity, making it a vital habitat for various cetacean species. To investigate the diversity of cetaceans in the Beibu Gulf during the summer, as well as the distribution of the only commonly observed large cetacean in the region—the Eden’s whale (Balaenoptera edeni edeni), this study collected water samples from 12 sites in the Chinese waters of the Beibu Gulf from July to August 2023, and utilized environmental DNA technology to detect the composition of cetacean species. The results indicated that 3 cetacean species were detected in the Beibu Gulf during the summer, including the Indo-Pacific finless porpoise (Neophocaena phocaenoides), the pantropical spotted dolphin (Stenella attenuata) and the Indo-Pacific bottlenose dolphin (Tursiops aduncus). The species with the highest number of positive detection sites (N) was the Indo-Pacific finless porpoise (N = 5), which was found throughout the Beibu Gulf; followed by the pantropical spotted dolphin (N = 4), which was distributed in the central and southern regions of the Beibu Gulf; the Indo-Pacific bottlenose dolphin had the fewest detection sites (N = 1), located in the central part of the Beibu Gulf. Therefore, the central Beibu Gulf during summer may serve as a hotspot habitat for cetaceans. Neither high-throughput sequencing nor specific sequencing for Eden’s whales detected the presence of this species, suggesting that all Eden’s whales around Weizhou Island may have left the Chinese waters of the Beibu Gulf during summer. The research results have enriched the understanding of cetacean diversity and distribution in the Beibu Gulf, enhancing baseline information for the conservation of cetaceans in the region.