I have reviewed the manuscript entitled "Estimating the extended and hidden species diversity from environmental DNA in hyper-diverse regions". Species inventory is the most important first step for biodiversity conservation. However, there are many areas that are known to have very high biodiversity, such as tropical coral reefs, but have not been fully investigated. In this manuscript, authors developed a method to quantitatively investigate extended and hidden species diversity by using a combination of under water visual census (UVC) and environmental DNA (eDNA) metabarcoding surveys. The framework developed by the authors can be used to develop guidelines for future biodiversity conservation, and is therefore useful. Environmental DNA analysis has been performed with high quality and there are no experimental problems. However, I have several concerns as below.

1. Is a sample size of 92 sufficient to cover this broad and very diverse area? In particular, as shown in Fig. 2, the areas where UVCs were conducted for comparative analysis are geographically very large, and the significance of comparing them with this environmental DNA sample should at least be discussed.

2. Related to the above, the lack of overlap between areas where eDNA sampling and UVCs were conducted increases hidden and extended diversity. It increases the uncertainty of such estimates shown in FIg. 5. This point should also be discussed.

3. The volume of discussion is too small. The authors have a huge data set and could have discussed a lot more. For example, the authors mention in only one sentence that pelagic piscivorous species tend to be missing from the check list, and it would be possible to discuss the weaknesses of such traditional survey methods (which could be considered a strength of eDNA analysis).

In conclusion, this manuscript, while excellent in the experiments and analysis, is insufficient in its discussion and the above points should be discussed to make the manuscript better.

I have re-reviewed the manuscript entitled "Estimating the extended and hidden species diversity from environmental DNA in hyper-diverse regions". The authors addressed all previous concerns raised in the previous review round. However, However, I feel that the discussion on research limitations might be better written more explicitly. This is more a matter of linguistic sense than a logical one, and I would like to leave the judgment to the editor.