This study assessed the safety and quality of some fermented foods in Egypt. The fermented milk (yogurt), sour milk (Laban Rayeb) and flour fermented barley (Buza or Boza) samples were collected from Sharkia Governorate (Zagazig, Faqous, Abu Kebir and El Husseiniya District), Egypt. Total bacterial diversity, lactic acid bacteria, yeasts and molds, staphylococci and micrococci, coliforms, Enterobacteriaceae, pseudomonads and enterococci counts within each sample were determined. The identity of the isolates was established through microscopic, biochemical and molecular techniques. The total bacterial counts and lactic acid bacteria of analysed samples ranged from 6.70 to 9.23 log cfu/ml and 6.09 to 9.24 log cfu/ml, respectively. The overall results on the bacterial biota of the fermented foods revealed that total bacterial loads of yogurt, Laban Rayeb and Boza were 8.30, 9.23 and 8.19 log cfu/ml, respectively. Generally, results revealed that undesirable bacterial isolates from de Man, Rogosa, and Sharpe agar (MRS) and M17 selective media for lactic acid bacteria belonged to Bacillus, Pseudomonas and Staphylococcus genera and fungal isolates belonged to Saccharomyces and Candida. genera. The most dominant bacterial species identified by 16S rRNA sequencing analysis were B. sporothermodurans, B. thuringiensis, B. safensis, B. sphaericus B. tequilens, B. licheniformis, B. vietnamensis, B. amyloliquefaciens, B. subtilis,  P. psychrotolerans, S. cohnii and S. saprophyticus. This study proved the presence of unusual bacteria contaminants (UBC) in the selected fermented foods. The UBSs could be pathogenic and/or toxigenic by producing various types of toxins.