The internal transcribed spacer  (ITS) region is highly variable between species and its pretty easy to amplify (due to high copy number). There are many successful fungal ITS primers in the literature and its pretty well represented in molecular databases such as NCBI and Unite. 

Hi Laurensius,

The answers above are correct in that the 18S is more conserved and the ITS is highly variable. Depending on the research question you want to answer, you may want to choose one or the other or perhaps, both. I was performing high throughput sequencing and most research amplifies the fungal metagenome using ITS primers. There are a few drawbacks from using the ITS primers but again, it depends on the research question you are trying to answer. For fungal culturing work it is a good idea to perform PCR for both the 18S and ITS region. Typically speaking the 18S is good to identify to the genus level and the ITS will resolve differences at the species level.

For 18S I use edel-hermann primers and for ITS I use the ITS1 and ITS4 for culturing and ITS1 and ITS2 for Illumina sequencing.

Good luck!

Laurensius

It depends on your question

18s is very conserved so it is good to reconstruct the history of clades, this is, for phylogeny. However now it is not used very frequently. There are other regions that are better for this purpose as de LSU (28s).

ITS is very variable and it usually is good (particularly in Basidiomycetes) to separate species and for molecular identification. That is why it is the official barcode genetic marker for fungi:

http://www.pnas.org/content/109/16/6241