Did you try doing a nucleotide BLAST search? http://blast.ncbi.nlm.nih.gov/Blast.cgi

Dear Yordanis, 

Thomas' suggestion would be very helpful. If you need ITS sequences of species related to one organism of interest, you can BLAST its ITS sequence and you will get a list of the closest relatives represented in GenBank. BLAST search results include links to download the sequences of all closest relatives. 

If you are interested in a particular group of organisms, e.g. the fungal genera Alternaria, Cladosporium or Trichoderma, big revisions of them have been published in Studies in Mycology and other journals, and the alignments used in the phylogenetic analyses have been deposited in TreeBASE (https://treebase.org/treebase-web/home.html). You can download the complete alignments from TreeBASE with many species, without the need to compile the sequences one by one as you would need to do from GenBank.

Success with your research!

Hugo 

Thank you both Thomas Marcussen and Hugo Madrid for your answers. I'm very sorry if my question seemed trivial, therefore please allow me to elaborate further:

I want to construct a tree from around 300 Fungal species from the orders Ascomycota and Basidiomycota that have their genomes sequenced and deposited in the JGI MycoCosm database (http://genome.jgi.doe.gov/programs/fungi/index.jsf). I just don't want ANY specie, but the ones I need for my study. Hugo's suggestion for looking in TreeBase led me to AFTOL database (http://www.aftol.org/data.php), which I had seen earlier but dismissed. There are some data from previous studies on fungal phylogeny. Still, I can not procure the entire dataset I need. That prompted my question in this forum.

I've tried BLAST (both blastn and megablast) using (as example) ITS from Trichoderma sp. and the results of the first 100 hits belong to Trichoderma genus. That does not suit my needs. Iterative Blast is not suitable either. If there is a more appropriate way to conduct Blast for this particular purpose, please let me know.

Once again, thanks for your answers.

Best regards,

Yordanis