Fungal infections are one of the most common life-threatening diseases amongst immunodeficient individuals. Invasive fungal disease is most commonly treated with an azole antifungal agent. This is likely to result in selection pressure with a subsequent increase in azole resistance in a variety of fungal pathogens. Antifungal resistance is associated with higher mortality rates (88%) and treatment failure is frequent. This makes the current clinical management of fungal disease very challenging. Clinical isolates from a variety of fungal species have been shown to contain mutations in the MSH2 gene, which encodes a component of the DNA mismatch repair pathway, which when mutated results in an elevated mutation rate. An elevated mutation rate can increase the opportunity for selectively advantageous mutations to occur, resulting in the development of antifungal resistance. In this study we aimed to characterise the molecular mechanisms causing azole resistance in Cryptococcus neoformans by whole genome sequencing of antifungal drug resistant strains isolated from a msh2∆ mutant. The genomes of resistant strains did not possess mutations in the gene encoding the target of azoles, ERG11, suggesting ERG11- independent pathways of resistance in C. neoformans. The results suggest that antifungal resistance in C. neoformans is due to the small contributions from mutations in many genes rather than to large contributions from mutations in a few genes. The polygenetic basis for azole resistance in C. neoformans raises concerns about the ability to use molecular markers for rapid diagnosis and for the management of resistant strains.