The main purpose of this study was to analyze and identify the species of fish eggs from the Jiangmen marine environment in summer, based on DNA barcoding technology. In the present study, we acquired a total of 217 effective mitochondrial COI sequences from fish eggs, and the success rate of sequencing was up to 68.5%. After the alignment of the BOLD database, we found that besides 2 species, a total of 5 orders, 14 families, 19 genera, and 20 species were identified. Statistical analyses showed that the interspecific genetic distances were 0~0.006, and mean interspecific genetic distance was 0.002, whereas the intraspecific genetic distances were 0.149~0.325, and mean intraspecific genetic distance was 0.255, which was 128-fold higher than the former. Among the fish eggs, the most abundant order was Perciformes (51.8%), followed by Clupeiformes (24.8%); the most abundant species was Megalaspis cordyla, , and . In this investigation, the most abundant fish eggs were found in eastern Chuanshan Archipelago, both in numbers and species. The Chuanshan Archipelago is also known as the main spawning site of . However, nearly no fish eggs were found in the Huangmao Bay area or western Zhenhai Bay, possibly owing to environmental disruption and a decrease of effective parent number, triggered by environmental variation and contamination from land-sourced pollutants. In general, we revealed the distribution pattern of fish eggs from the Jiangmen marine environment in summer, which provided a theoretical basis for developing effective protective measures for spawning sites. Meanwhile, the results also showed that DNA barcoding technology could be effective and broadly applied to identify the species of fish eggs in the marine habitats of our country.