Abstract:[Background] Bacillus amyloliquefaciens SQ-2 is a probiotic strain isolated from commercially available watercress paste, with previous experiments demonstrating its exceptional bacteriostatic ability against plant pathogenic fungi, indicative of strain SQ-2’s rather good bio-control abilities and potential application prospects in bio-pesticides. [Objective] To explore the genetic information of B. amyloliquefaciens SQ-2, and divulge its antifungal mechanism. [Methods] The whole-genome sequencing of strain SQ-2 was performed on an Illumina MiSeqX10 platform. Raw data were cleaned using Trim Galore v.0.4.0 and examined for quality using FastQC. In addition, de novo assembly was performed using the SOAPdenovo2 package. Genes responsible for the biosynthesis of secondary metabolites were identified using antiSMASH. [Results] The genome of B. amyloliquefaciens SQ-2 was 3 486 537 bp with the average guanine/cytosine (GC) content of 46.63%, which potentially coded 4298 genes. Eleven gene clusters related to secondary metabolite biosynthesis were discovered, of which six were identified as antifungal synthesis clusters, encoding bacillaene, bacilysin, butirosin, fengycin, bacillibactin, and surfactin, respectively. The sequencing data from this article were submitted to the NCBI and were available in the GenBank database (Login No. JAHXSB000000000). Ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis indicated that the surfactin, bacillibactin, and bacillaene were produced by strain SQ-2. [Conclusion] This study presents the genome sequence of B. amyloliquefaciens SQ-2, and it exhibits intense antagonistic activity against plant pathogenic fungi. The entirety of this genome sequencing study can assist in utilizing known antifungal peptides and searching for novel antifungal substances to combat pathogens.