Use D1/D2 sequencing in place of the ITS region, or expand the amplified region to include some of the 18s or 28s regions.

You could try amplifying the D1/D2 region of 26S using primers NL1 / NL4 (Kurtzmann & Robnett, 1997)

NL1: 5’-GCA TAT CAA TAA GCG GAG GAA AAG-3’

NL4: 5’-GGT CCG TGT TTC AAG ACG G-3’

This region is often used for yeast species identification (especially clinical isolates), so there should be fair number of sequences available in the databases.

Dear Alexander Piper

In my knowledge the (ITS1 and ITS2) and the 5,8S rRNA is accepted as a powerful method for species identification. ITS2 is a good one for sp. identification

http://sites.biology.duke.edu/fungi/mycolab/primers.htm

http://www.formatex.org/microbio/pdf/pages783-787.pdf

Thank you 

Thankyou for your answers, i am going to go ahead and try sequencing the D1/D2 Regions as well

Alexander, another interesting tip when doing ITS BLAST is to use the refseq dataset to query against a verified database. Have a look at the paper of Schoch et al. (2014).

Best of luck

http://database.oxfordjournals.org/content/2014/bau061