Two techniques have been described that use the polymerase chain reaction (PCR) to amplify many arbitrary regions of a genome simultaneously. Regions amplified by these techniques are generally polymorphic among closely related species and are beginning to be used in molecular taxonomy. In this chapter I discuss the positive and negative aspects of using arbitrary regions for taxonomy and describe strategies to adopt in overcoming some of their major disadvantages. I discuss how to set up a dataset of arbitrarily primed polymorphisms (APP) and demonstrate how cluster analysis of this dataset can be used to test marker specificity. Once an APP dataset is established, cluster analysis provides a simple means to routinely identify field collected specimens.
