Anything under 97% would be considered a new species. It is always a good idea to sequence the 18s and the ITS region for fungi. The ITS region is not nearly as conserved as the 18s region is and it would strengthen your story if you do indeed have a new species.

Thank you Cloutier, can you also explain to me whats the minimum percentage to determine that the isolate is same species or same genus and the refrence about it?

Dear Fatia

for species difference or new species   - less than 97 %

more than 97 % same genus or species 

Follow my publications 

https://scholar.google.co.in/citations?user=PSoYZ6MAAAAJ&hl=en&authuser=1

Fatia, I am not sure what the % requirement is to define a new genus, but I do know that if the species is ~92/93% identical to another known species then you can argue that you have a new order. So, I would assume that to classify a new genus then the identity would be close to 95%. If you think that you have a new genus, I highly recommend performing DNA barcoding on the ITS region. Reviewers will most likely want that information for fungal classifications.

For fungi, most of the time you classify a new genus by morphology and physiology and use the DNA barcode to strengthen your argument. Most people use PDA agar for the morphological tests.

I have attached a few papers that might interest you.

Good luck!

okay, thank you Bhushan and Cloutier.

this was helping me.

You can not trust BLAST results even had 100% identity for species identification. Also  you need to determine phylogenetic position of your fungi by using MEGA software. To achieve this aim, download all the BLAST hit and construct a phylogenetic tree. 

Blast is a tool for exploratory data, its results depend on the sequence quality, some times the call base from the sequencer is not accurate, then it should not be a conclusive in the species delimitation. The use of filogenetic approach can give more accurate determination. However it is important that you combine diferent characteristics such as morfology and biology in the final analysis, in order to know if the differences that you found a molecular level are enough to family o genus delimitation.

thank you very much çelik and Leon, that was very helping me.