A variety of methods have emerged for genetic fingerprinting the infectious fungi. One of the most versatile is Southern blot hybridization with species-specific complex DNA probes that include sequences that identify hypervariable, moderately variable and invariant genomic sequences. These probes assess genetic relatedness at all the necessary levels including identical, highly related but non-identical, moderately related and unrelated. Methods are described for cloning complex probes, characterizing them and verifying their effectiveness at the different levels of resolution. The complex probes that have been developed for Candida albicans, C. glabrata, C. dubliniensis, C. tropicalis, C. parapsilosis and Aspergillus fumigatus are described and discussed.