Many genetic and phenotypic changes occur during the development of drug resistance in fungi. A straightforward approach to assess the contribution of a specific gene to drug resistance is to examine its inactivation in a resistant isolate and to analyze the effect of the mutation on the resistance phenotype. The generation of knockout mutants in the diploid yeast Candida albicans requires two rounds of gene replacement to inactivate both alleles of a target gene. Because auxotrophic markers are not useful for the genetic manipulation of wild-type, clinical isolates, dominant selection markers are required. In this chapter, we describe the MPAR flipping method that combines dominant selection with recombinase-mediated marker recycling for targeted inactivation of specific genes in C. albicans wild-type strains. Using the MPAR flipper makes drug-resistant clinical isolates amenable to genetic manipulation, a prerequisite for the study of causal relationships between specific genes and drug resistance.