It is sometimes necessary to assess the genetic relatedness of isolates to identify the origin of an infection. In addition, evidence is accumulating that drug resistance can be associated with strains from a particular clade and that strains can exhibit anatomical specificity. It may, therefore, be valuable in the near future to screen for strains with a propensity for drug resistance. While a number of methods exist for genetically fingerprinting the infectious fungi, only a few provide the necessary resolution not only for distinguishing whether strains are highly related or unrelated, but also for grouping a strain in a particular clade. Here, we provide the procedures for performing the two methods that have proven most effective in the past 5 years: Southern blot hybridization of restriction fragments with complex probes and multilocus sequence typing (MLST).