A number of studies in plant pathology require the ability to distinguish fungal isolates. Such differentiation is often complicated by a lack of morphological or obvious phenotypic differences and by the impracticality of full-scale infection studies. The polymerase chain reaction (PCR) has provided a venue to establish rapid diagnostic tools for fungal pathogens and to facilitate within-species comparisons. This article will review tools derived from PCR and explore their applications to such fungi. The strengths and limitations of each method will also be discussed.