Sea temperatures are rising. Japanese coastal waters in particular have seen a rise of 1.28°C over the last 100 years, which is around double the increase of 0.61°C in the global average. The habitats of a variety of marine organisms have changed over this period, and the conventional ecosystem balance is breaking down. Climate change is thought to be a factor in this, but the precise reasons are still unclear at this stage. However, using environmental DNA microanalysis, it has become possible to gain an accurate understanding of current ecosystems without capturing living creatures. By learning what kinds of organisms inhabit Japanese coastal waters, we will be able to make the coastal fisheries industry more efficient.