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Streptomycin applications are essential for the control fire blight in New York. Recent development of streptomycin resistance in New York strains of <i>E. amylovora</i> poses an immense challenge for future disease management. Our goals were to <b>(</b>1) investigate the diversity of New York strains of streptomycin resistant (SmR) and streptomycin sensitive (SmS) <i>E. amylovora</i> to determine the status and origin of SmR <i>E. amylovora</i>, and 2) investigate how increasing applications of streptomycin and kasugamycin directly affect epiphytic bacterial populations in the apple phyllosphere. Amplification and sequencing of CRISPR region DNA was used to examine <i>E. amylovora</i> strain diversity in New York and to compare NY <i>E. amylovora</i> strains with SmR <i>E. amylovora</i> from other locations world-wide. Results have provided evidence for the likely introduction of SmR strains from other areas into NY and also for resistance development within NY orchards. Field trials conducted with increasing antibiotic applications followed by identification and enumeration of epiphytic bacteria from treated apple leaves were used to elucidate the effects of antibiotics on bacterial populations. Results have shown that increased applications of both streptomycin and kasugamycin have a significant impact on community structure and population size of epiphytic bacteria in the apple phyllosphere.