Fire blight is a serious disease of apple and pear trees caused by the bacterium, Erwinia amylovora. This bacterium harbors a pathogenesis mechanism known as the Hrp secretory operon which induces some resistance genes and suppresses other resistance genes in the host plant following invasion. While previous researchers analyzed expression of defense genes in apple flowers on detached branches maintained in water (Venisse et al 2002), I used a novel method to examine gene induction in flowers on whole trees. In addition to an avirulent mutant of the pathogen, I also applied biological control agents of fire blight Pseudomonas fluorescens A506 and Pantoea agglomerans C9-1 to flowers to analyze the defense response of apple trees to nonpathogenic epiphytic bacteria. Plant resistance-related proteins were induced early after inoculation with the bacterial treatments, confirming that these genes are part of an immediate defense response. However, since the regulation of genes expressing enzymes in the phenylpropanoid pathway, chalcone synthase and chalcone isomerase, was not limited as a response to colonization by Erwinia amylovora, the expression of these genes may not be dependent on a hrp cluster. The difference in results from previous research may illustrate the variability of plant defense behavior in a changing environment.