Over the past decade, environmental DNA (eDNA) analysis has been developed and applied to various studies. However, there is still a lack of basic information on eDNA, especially relating its physiological state and source. As the first step for the elucidation on eDNA, we tried visualization of nuclear genomic DNA in tissue and water samples from Japanese Jack Mackerel (Trachurus japonicus). We kept the fish in 500-L tanks, and collected water samples from the tanks and gill samples from the fish. After slide preparation, we performed genomic in situ hybridization (GISH), which enables the species-specific visualization of the entire nuclei. As a result, we achieved to visually detect the Japanese Jack Mackerel’s nuclei from both gill and water samples. The size and form of the nuclei appeared to be similar between tissue and water samples, and they were about 5 µm in diameter. Our results suggest that a part of fish eDNA could remain in water as the cellular or membrane-bound DNA, and thus would survive from various degradative processes in natural environment. The cytogenetic approaches might contribute to understand how eDNA could be in aquatic environment.