very less chance to get polymorphism within same isolates. you can run but it is meaning less. if any new mutation is generated within sample than again it is very difficult to detect through RAPD. by chance you may get polymorphism.

You can do it, but it will give you (most of the time) non significant results. I don't know what's the exact case with your fungus but if it does not have a very high mutation rate then you probably won't find polymorphisms by RAPDs.

I'd suggest using SNPs, the sensitivity of the technique is better and you won't have the problem of "dominance" that you'll find with RAPDs, also, whith rapds the interpretation of the results (if any) is not so straight forward.

Thankyou Gustavo Rodriguez Alonso and Tejas Bosamia