Over the last decade, environmental DNA (eDNA)-based bioassessment has emerged as one of the most rapidly evolving and widely adopted methodologies in biodiversity research. In this context, we present a comprehensive overview of the eDNA research field based on a bibliometric analysis of 4524 documents published between 1992 and 2024. The journals with the most published articles on eDNA were Environmental DNA, PLOS ONE, and Molecular Ecology Resources. The countries with the most eDNA publications were the United States, China, and Japan. The structural topic modeling method employed allowed us to identify the main research topics, their interrelationships, and their temporal dynamics. Based on the temporal change in research topics, the application of eDNA research has shifted from methodological research to biodiversity and community research since 1992. The results were interpreted to provide insights into the current state of the eDNA research field, shedding light on the advancements, challenges, and potential applications of eDNA metabarcoding.