Within Biological Resource Collections, the successful long-term storage of fungal cultures is essential because of their scientific and potential commercial value. Preservation procedures such as cryopreservation have traditionally been used to ensure genomic stability due to the suspension of metabolic activity at ultra-low temperatures. Genomic integrity is important with regards to conservation, as changes in the genome may compromise production of a desired metabolite, enzyme or activity. To evaluate cryopreservation as a conservation protocol, genomic integrity was assessed in five strains of the economically important fungus Trichoderma. Two polymerase chain reaction (PCR) fingerprinting techniques commonly used for molecular studies of fungi were applied. Three genetic polymorphisms were detected amongst replicates post preservation, indicating that even robust, standardised preservation cryopreservation methodologies can sometimes induce genomic change. However, the low number of polymorphisms suggests that cryopreservation is a reliable method for organism storage over long periods of time.