Isozyme analysis is a powerful technique for assaying genetic variation within and among populations. This versatile approach has been used on bacteria, fungi, plants, and most major groups of animals, from insects and other invertebrates to fish and mammals. The appeal of isozyme analysis stems from its ease of use, low cost, and speed. DNA-based technologies can provide a higher level of polymorphism with concomitantly greater resolution. However, when sufficient variation is present, isozymes provide the fastest, easiest answers to biological questions at a significantly lower cost compared to other available techniques.

Isozyme analysis has a long history in the fungi. Differences among general protein patterns of species of Neurospora and Pythium were first noted during the early 1960s (Chang et al. 1962; Clare 1963). This approach developed into isozyme analysis with the application of methods for detection of specific enzyme activities. Since the mid 1960s, the technique has been applied to questions of fungal taxonomy, genetics, population biology, and species or strain identification (Micales et al. 1986; 1992) but it is only during the past 15 years that the true potential of the technique has been realized.

The purpose of this chapter is to introduce the concept of isozyme analysis in fungi. Strategies for developing new isozyme systems and for addressing particular questions about fungal taxonomy, genetics, and population biology will be discussed. Particular emphasis will be placed on identifying common pitfalls and barriers to successful implementation of new isozyme systems, especially interpretation of banding patterns, preparation of tissue samples, and methods and approaches to data analysis. Specific examples of isozyme analysis for the major groups of fungi will be discussed to illustrate the many potential applications of this extremely useful and powerful technique.

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