Microbes which exhibit an elevated mutation rate, termed mutators, are found in natural populations of pathogenic microbes. A mutator phenotype is advantageous in rapidly changing or stressful conditions such as those experienced in a host, as it allows the rapid accumulation of beneficial mutations which aid in adaptation. In fungal pathogens, mutation of the MSH2 gene of the DNA mismatch repair pathway leads to a mutator phenotype and the rapid emergence of resistance to antifungal drugs. The objective of this study was to investigate the molecular mechanisms underpinning the emergence of resistance in the fungal pathogen Cryptococcus neoformans. The genome sequences of independently isolated antifungal drug resistant and multi-drug resistant MSH2 strains revealed abundant, universal point mutations in genes involved in gene regulation, membrane transport, cellular signalling, epigenetic modification and DNA stability, as well as, changes in euploidy. This study suggests there are common molecular mechanisms leading to the evolution of antifungal drug resistance in mutator strains.