Bacillus amyloliquefaciens YP6, a plant growth promoting rhizobacteria, is capable of efficiently degrading a wide range of organophosphorus pesticides (OPs).  Here, we report the complete genome sequence of this bacterium with a genome size of 4 009 619 bp, 4 210 protein-coding genes and an average GC content of 45.9%.  Based on the genome sequence, several genes previously described as being involved in solubilizing-phosphorus, OPs-degradation, indole-3-acetic acid (IAA) and siderophores synthesis.  Interestingly, compared with the genomes of B. amyloliquefaciens species, strain YP6 had larger genome size and the most protein-coding genes.  Moreover, the four categories of “cell envelope biogenesis, outer membrane (M),” “translation, ribosomal structure and biogenesis (J),” “transcription (K),” and “signal transduction mechanisms (T)” were fewer.  These differences may be related to extensive environmental adaptability of the genus B. amyloliquefaciens.  These results expand the application potential of strain YP6 for environmental bioremediation, provide gene resources involved in OPs degradation for biotechnology and gene engineering, and contribute to provide insights into the relationship between microorganism and living environment.