Abstract: In order to isolate and preserve lactic acid bacteria strains in naturally fermented foods and enrich the diversity information of lactic acid bacteria in naturally fermented foods, pure culture method and Metagenomics 16S rRNA gene sequencing technology were used to isolate, identify lactic acid bacteria and study their diversity in fermented olive juices collected from Morocco in this paper. The results showed that 52 strains of lactic acid bacteria were isolated and identified from 2 fermented olive juices samples, belonging to 3 genera and 4 species. Lactococcus lactis was the dominant strain in fermented olive juice, occupying 42.31% of the total isolates. The strains of Lactobacillus plantarum and Enterococcus were also isolated. Based on PacBio SMRT sequencing technology, bacteria in olive juice were classified into 5 phyla, 40 genera and 80 species. The dominated strains were also Lactococcus lactis, in addition, Lactobacillus plantarum and Lactobacillus casei were also detected.