Dear Marwa, if there SSR markers are available in mushrooms, you can use it for diversity, fingerprinting and phylogeny analysis easily. plz see this paper- World J Microbiol Biotechnol (2010) 26:527–536 and Appl Microbiol Biotechnol. 2009 Oct;84(6):1125-35. i hope this will help you.

Thanks a lot, in fact I did go through the article you recommends (online view), although it is not downloadable or I may fail to find a link to download. The article is very excellent, However, They used SSR markers for a specific species (Lentinula edodes). but I have to study all mushroom types common in our area.which may fall under 4 or 5 genus. I'm willing to use SSR because of its advantages. can I use it in my case? and can I use Databases to develop SSR markers to merge between the most common types?

Also, more general:

http://tiny.cc/qmuomw