Several methods are currently available for the identification and differentiation of Erwinia arnylovora, the bacterium which causes fire blight. Historically, many laboratories have relied upon diagnostic medias or subtle differences in nutritional requirements to identify and distinguish plant pathogenic bacterial species. However, diagnostic protocols exploiting recent advances in molecular biology have become readily available to the phytobacteriologist. Specifically, the polymerase chain reaction (PCR) affords a rapid and reliable approach to identify and differentiate strains of E. amylovora as they are isolated from novel fire blight outbreaks. Three techniques, in particular, have been developed either specifically for use with E. amylovora or have been applied to the fire blight bacterium after being used to characterize other veterinary or medically significant prokaryotic systems. These techniques have been designated as follows: i) pEA29 PCR, ii) 'ribotyping', and iii) REP PCR. Below, we discuss the backgrounds associated with these rapid molecular genetic techniques and present detailed protocols for the three techniques in a single unifying format.