Bacillus spp. are promising candidates for biological control of postharvest diseases. Bacillus amyloliquefaciens PG12 was isolated from apple fruit and exhibited broad-spectrum antifungal activity. Botryosphaeria dothidea was significantly suppressed by PG12 in in vitro and in vivo. Lumpy appearance and abnormal structure of the mycelia from the edge of inhibition zone were observed using scanning electron microscopy (SEM) in in vitro assays. Furthermore, the lipopeptide crude extracts from cell-free supernatant of PG12 had remarkable antifungal activity against B. dothidea, indicating that lipopeptides played a major role in the biological control ability of PG12. PCR detection revealed that PG12 harbored the gene clusters required for the biosynthesis of the two main families of lipopeptide, including iturin and fengycin. One iturin-like compound (Rf 0.4) showed inhibitory activity against B. dothidea using thin layer chromatography (TLC)-bioautography analysis and were further fractionated by semipreparative high performance liquid chromatography (HPLC). The fraction with a molecular weight of 1043.55 m/z was identified as iturin A by electrospray ionization quadrupole-time-of-flight mass spectrometry/mass spectrometry (ESI-Q-TOF MS). Taken together, B. amyloliquefaciens PG12 was an effective biocontrol agent against apple ring rot caused by B. dothidea and iturin A was an important factor in its activity.