Gnathopogon caerulescens is an endangered but commercially important fish in Lake Biwa, Japan. The population size of G. caerulescens has drastically reduced in the past decades, and there is a strong need to develop effective resource management frameworks for the sustainable use of this species. In the management of endangered species, it is important to monitor and grasp their distribution and abundance. Although catch-based methods have generally been employed for this purpose, these methods require more labor and time and can damage the populations of endangered species. In this study, we aimed to develop a rapid and non-invasive monitoring tool for G. caerulescens using an environmental DNA-based approach. We developed a real-time PCR assay that specifically detects and quantifies G. caerulescens DNA and applied the developed assay to monitor the concentrations of G. caerulescens DNA in water in Lake Biwa. The dynamics of G. caerulescens DNA concentrations well reproduced the main characteristics of life history of G. caerulescens, suggesting the promising use of environmental DNA-based methods for monitoring the distribution and abundance of this species.