best to use internal primers and concatanate the sequence. There are alot of ITS-5.8S region primers available. it should give you 80 bp fragment amplifications which can be put together to get the full sequence. qPCR using certain specific primers can also work. Good luck. 

Hi, see this paper:

Controversy over Hygrophorus cossus settled using ITS sequence data from 200-year-old type material

By:Larsson, E (Larsson, E); Jacobsson, S (Jacobsson, S)

MYCOLOGICAL RESEARCH

Volume: 108

Pages: 781-786

Part: 7

DOI: 10.1017/S0953756204000310

Published: JUL 2004

Hi, Sam

Above recommandations are OK. In first, try to see if you can get ITS1 and ITS2 separatly, by testing different pairs of primers (http://sites.biology.duke.edu/fungi/mycolab/primers.htm). If you believe that you have to sequence smaller fragments you can develop more specific primers based on sequences of presumed closely related taxa.

Nested PCR might also works

I noted that, unfortunatly, samples from certain herbaria are more degraded than from others.

I would also recomend to perform the extraction with a good kit. To me the best is the E.Z.N.A Fungal DNA Mini Kit,Omega bio-tek.

Good luck!

Dear Samantha Karunarathna, above recommendations are correct. I fully agree with Valerie Hofstetter opinion.

Best regards

Vladimir