Recently, strategies for controlling <i>Fusarium oxysporum</i> f. sp. <i>lycopersici</i> (<i>Fol</i>), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol agents. In this study, an analysis of the biocontrol and plant growth promoting (PGP) attributes of 11 isolates of loamy soil <i>Bacillus</i> spp. has been conducted. Among them, the isolates B.PNR1 and B.PNR2 inhibited the mycelial growth of <i>Fol</i> by inducing abnormal fungal cell wall structures and cell wall collapse. Moreover, broad-spectrum activity against four other plant pathogenic fungi, <i>F. oxysporum</i> f. sp. <i>cubense</i> race 1 (<i>Foc</i>), <i>Sclerotium rolfsii, Colletotrichum musae,</i> and <i>C. gloeosporioides</i> were noted for these isolates. These two <i>Bacillus</i> isolates produced indole acetic acid, phosphate solubilization enzymes, and amylolytic and cellulolytic enzymes. In the pot experiment, the culture filtrate from B.PNR1 showed greater inhibition of the fungal pathogens and significantly promoted the growth of tomato plants more than those of the other treatments. Isolate B.PNR1, the best biocontrol and PGP, was identified as <i>Bacillus stercoris</i> by its 16S rRNA gene sequence and whole genome sequencing analysis (WGS). The WGS, through genome mining, confirmed that the B.PNR1 genome contained genes/gene cluster of a nonribosomal peptide synthetase/polyketide synthase, such as fengycin, surfactin, bacillaene, subtilosin A, bacilysin, and bacillibactin, which are involved in antagonistic and PGP activities. Therefore, our finding demonstrates the effectiveness of <i>B. stercoris</i> strain B.PNR1 as an antagonist and for plant growth promotion, highlighting the use of this microorganism as a biocontrol agent against the Fusarium wilt pathogen and PGP abilities in tomatoes.