During 2006 and 2007, fruit thinning effects of three plant growth promoting rhizobacteria (PGPB) strains (Bacillus OSU-142, Microbacterium R2(3) and Bacillus T7) and NAA (10 and 20 ppm) were tested in apple cvs. Golden Delicious and Braeburn in terms of fruit setting, yield, fruit weight, fruit firmness, total soluble solid (TSS), titratable acidity and shoot length in the province of Konya, Turkey. Bacterial strains were sprayed at 7, 14 and 21 days after full bloom, and NAA was sprayed at 21 days after full bloom. The results showed that NAA and bacterial treatments decreased fruit setting and number of fruit per tree at various ratios in both cultivars. The lowest fruit setting cvs. Golden Delicious and Braeburn were obtained from 20 ppm NAA treatment in both years. Among the bacterial treatments R2(3) (24.1% in 2006 and 39.1% in 2007) in Golden Delicious and R2(3) (11.6% in 2006) and T7 (17.3% in 2007) in Braeburn gave the lowest fruit setting ratio while fruit setting ratio in Golden Delicious and Braeburn were 36.7 and 46.2% (2006) and 12.8 and 28.2% (2007) in the control, respectively. The highest fruit number was found from the control in both cultivars and years. Fruit yield was significantly decreased in Golden Delicious by NAA treatments but not affected in Braeburn by thinning. The highest yield was found from the control in cvs. Golden Delicious and Braeburn in both years. However, fruit weight was significantly increased by NAA and bacterial treatments. While the lowest fruit weight was in the control in both cultivars and years, the highest fruit weight was in R2(3) in Golden Delicious (164.6 g in 2006) and T7 (138.7 g in 2006) and OSU-142 (173.5 g in 2007) treatments in Braeburn. Treatments of R2(3) and T7 significantly increased fruit firmness in Golden Delicious and Braeburn in both years, respectively compared with the control. NAA and bacterial applications also significantly increased TSS in Braeburn but not Golden Delicious. The results of this study suggest that Bacillus OSU-142, Microbacterium R2(3) and Bacillus T7 have the potential to be used as fruit thinning agents under organic and sustainable growing conditions on apple.