Species of Bacillus and Brevibacillus associated with honey bees are interesting sources of bioactive compounds with potential uses beyond the field of apiculture. Most Bacillus species and related genera produce a broad range of antimicrobial compounds, with activity against bacteria and fungi that include peptides, lipopeptides, bacteriocins, and bacteriocin-like inhibitory substances. By using biological tools, we evaluated the antagonistic activity of 34 bacterial strains against Paenibacillus larvae and Ascosphaera apis, the causal agents of American Foulbrood and Chalkbrood diseases of honey bee larvae, respectively. Data reveal that the antagonistic response was strain-specific, species-specific, and also medium-dependent. By using molecular tools, we investigated the distribution of antimicrobial peptide genes in the antagonist strains. The presence of homologous sequences to nine genes encoding for the synthesis of the antimicrobial peptides bacillomycin L (bmyB), fengycin (fenD), bacilysin (bacA), subtilin (spaS), iturin A (ituD, lpa-14; ituC), and surfactin (sfp; srfAA) was assayed by PCR. The distribution and frequency of these genes within the bacterial antagonists were also variable and strain-dependent, being the most common surfactins (srfAA = 44% and lpa-14 = 38%), iturins (ituD = 47%), and bacilysin (bacA = 32%). Moreover, a positive correlation between presence of antimicrobial peptide genes and antagonism was found taking into account that 85% of the antagonists had at least one of the antimicrobial peptide genes. We also identified those antagonists active against different P. larvae genotypes. To our knowledge, this is the first study of the association between the presence of homologous sequences of antimicrobial peptide genes and antagonism against P. larvae and A. apis strains.