This chapter discusses some major applications of isozyme analysis in basic and applied plant pathology. The technique is particularly useful with fungi; the greatest advances have been mostly with fungal pathogens. Isozyme banding patterns obtained from fungi are usually relatively uncomplicated and easy to interpret. Isozyme analysis can be readily performed in most laboratories with relatively little expense. With the development of computer programs that enable large numbers of comparisons at the gene level, much information can be obtained about the population genetics and life cycle of the organism. Isozyme analysis has proven particularly useful in situations where it is necessary to differentiate among two or more morphologically similar fungi. The chapter discusses other uses for isozyme analysis, along with advantages and disadvantages as compared to alternative techniques. Detectable isozymes can arise from three different genetic and biochemical conditions: multiple alleles at a single locus, single or multiple alleles at multiple loci, and secondary isozymes, usually arising from post-translational processing.