Bee honey have a highly intensity and specialized microbiota which plays an important role in metabolism, immunity, growth as well as development an antagonistic effect against pathogens. Thus, the aim of work was isolation genotype characterization of some strains of lactic acid bacteria (LAB) from fresh clover bee honey. Five samples of fresh clover honey were analyzed to detect the microbiome contents.  Dilution method and cultivation in selective media was used for counting of LAB strains, and the isolates were identified by their morphological characteristics that measured using Gram staining method and screened by catalase activity.   Furthermore, the morphological characteristics of bacterial cells were examined using Scanning Electron Microscope (SEM). The genotype of isolated strains was carried out by Polymerase Chain Reaction (PCR) method.  The results showed that, two novel bacterial strains of LAB were isolated from fresh clover bee honey. The strains of LAB which identified were; Lactobacillus brevis MK250013 and Lactobacillus casei MK250003.