Aims: This study aims to isolate and identify the indigenous bacteria of almonds fermentation.

Methods: Characterization of the indigeneous bacteria are using gram staining, biochemical tests, 16SrRNA gene sequencing, and the antimicrobial activity against Escherichia coli bacteria.

Results: Approximately 28 x 106 CFU / mL bacteria were obtained from almonds fermentations with 14 isolates from enrichment results. Three randomly selected isolates were gram-positive rod-shaped with a negative catalase and positive fermentation test. However, one isolate showed positive results on the motility test. The antimicrobial test results from the three randomly selected isolates using the disk diffusion method obtained inhibition zones of 7 mm, 6.7 mm, and 7 mm, respectively. Therefore, by using 16S rRNA gene sequencing, three different microorganisms were found, namely Bacillus subtilis strain IAM 12118, Bacillus Piscis strain 16MFT21, and Bacillus licheniformis strain BaDB27.

Conclusion: It was found that Bacillus subtilis strain IAM 12118, Bacillus Piscis strain 16MFT21, and Bacillus licheniformis strain BaDB27 in almonds fermentation and also can be used as probiotic bacteria.