A number of bacillus species have been recognized as effective and beneficial probiotics. However, some of the bacillus species are known to carry virulence genes which are the main cause of disease, hence, it is essential to evaluate their safety before considering them as probiotic. To date, in our country no studies have been performed on the genotypic virulence determinants of Bacillus species recognized as probiotics. In this study we aimed to assess the safety of indigenous bacillus species isolated from broiler chicken (Bacillus subtilis and B. leichniformis) and honey bee (B. subtilis and B. megaterium) samples. The selected bacillus species were identified based on biochemical and molecular, and evaluated for their probiotic properties such as acid and bile resistance, antimicrobial activity against Streptococcus agalactiae, Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, Salmonella typhimurium, Listeria monocytogenes and Escherichia coli, and antibiotic susceptibility pattern. The hemolytic activity, DNase, lecithinase, lipase, gelatinase, and coagulase activity were also studied. The presence of virulence genes, including hbl, Nhe, cytK, bceT, lipA, ces, was analyzed by molecular methods in a PCR reaction. According to results, all 11 Bacillus species showed considerable resistance to acid and bile, and appeared sensitive to all tested antibiotics. Seven isolates were beta hemolytic and lecitinase positive, one isolate was DNase positive, four isolates were cytK positive, while TA0044 and TA0046 were LipA positive. Only two isolates of poultry origin lacked all tested virulence genes and were classified as safe probiotic.