Electrophoretic karyotyping is a relatively new experimental technique whereby the chromosomes of lower eukaryotes are physically separated in an agarose gel matrix by pulsed field gel electrophoresis (PFGE), stained with ethidium bromide, and visualized when irradiated with ultraviolet light. The development of new instrumentation along with new methodology for preparing chromosome samples have greatly alleviated problems initially encountered in obtaining reproducible electrophoretic karyotypes. The key to obtaining high-resolution karyotypes resides in the identification of a successful method of preparing chromosomes for PFGE. The electrophoresis conditions are ultimately determined by the size of the chromosomes. That the number of chromosomes among field isolates of other fungal pathogens is variable is suggestive that aneuploidy may also play a significant role in karyotype variability. When an effective method of efficiently producing protoplasts is identified, the karyotypes may sometimes be characterized by diffuse bands with evidence of chromosomal fragments.