Species of Bacillus have the ability to synthesise different antimicrobial peptides (AMPs) and other compounds such as cell wall degrading enzymes which may be effective against various phytopathogens. This study aimed to detect AMP and lytic enzymes genes, by using biosynthetic gene markers, in a collection of rhizospheric and endophytic Bacillus spp. displaying significant inhibition of Leptosphaeria maculans in in vitro assays. Bacillus spp. were preliminarily identified by sequencing 16S rRNA genes. AMP screening of the selected Bacillus spp. was carried out using 10 primers to amplify genes encoding for antibiotics (surfactin, surfactin synthetase; iturinA, iturin C, two genes for , bacillomycin D, zwittermycin, fengycin) and lytic enzymes (chitinase, β-1,3-Glucanase) through polymerase chain reaction. The majority of strains possessed four to six genes of interest and strains with seven AMP and enzymes genes were also detected, however, none of the strains were positive for all 10 genes. Iturin A and Bacillomycin D were present most frequently among the selected Bacillus strains whereas the Iturin C encoding gene was the least often amplified. Interestingly, strain B94 (Bacillus amyloliquefaciens), the best performer in the in vitro assays, was found to carry the highest number (8) of AMP and lytic enzymes genes. Thus, selected AMP and enzyme gene markers may be useful for selecting putative bacterial biocontrol agents of phytopathogens.