Recently, with the development of genetic technology, interest in environmental DNA (eDNA) to study biodiversity according to molecular biological approaches is increasing. Environmental DNA has many advantages over traditional research methods for biological communities distributed in the environment but highly depends on the established base sequence database. This study conducted a comprehensive analysis of the habitat status and classification at the genus level, which is mainly used in eDNA (12S rRNA, 16S rRNA, 18S rRNA, COI, and CYTB), focusing on Korean registration taxon groups (phytoplankton, zooplankton, macroinvertebrates, and fish). As a result, phytoplankton and zooplankton showed the highest taxa proportion in 18S rRNA, and macroinvertebrates observed the highest ratio in the nucleotide sequence database in COI. In fish, all genes except 18S rRNA showed a high taxon ratio. Based on the Korean registration taxon group, the gene construction of the top 20 genera according to bio density observed that most of the phytoplankton were registered in 18S rRNA, and the most significant number of COI nucleotide sequences were established in macroinvertebrates. In addition, it was confirmed that there is a nucleotide sequence for the top 20 genera in 12S rRNA, 16S rRNA, and CYTB in fish. These results provided comprehensive information on the genes suitable for eDNA research for each taxon group.