Protocols that involve a freezing process are frequently used for the preservation of fungi, but there have been few studies to assess the physiological and genetic stability of isolates after preservation. In this study, the effects of cryopreservation and lyophilisation on the viability, physiology and genetic stability of isolates of Metarhizium anisopliae, Fusarium oxysporum and Serpula lacrymans were examined. It was found that preservation regime influenced the characters of some of the test isolates. Secondary metabolite profiles and extracellular enzyme production can be affected by preservation. Polymorphism's were detected after PCR fingerprinting in replicates of 2 isolates of Metarhizium that had been preserved by cryopreservation and lyophilisation. The results indicated a need to improve existing preservation protocols. Research is being undertaken to develop novel cryopreservation regimes for recalcitrant micro-organisms. Biochemical and molecular techniques will be used to assess the effectiveness of preservation.