Cassava plays an important role in the life and diet of several communities worldwide. It is used in various processed forms and has become the focus of research and innovation in recent years. Bioprocessing techniques, such as fermentation, have been utilized to create new avenues for its application in food and functional products. The fermentation of cassava can enhance its nutritional value, improve its shelf life, and increase its digestibility. However, the effect of salt-mediated fermentation on microbial diversity and potential benefits has not been widely reported. In this study, the effect of six levels of salt (NaCl), ranging from 0 to 25% after 50 days of spontaneous cassava fermentation at 25–30 °C, was investigated. A total of 30 bacterial isolates were selected for molecular characterization. A proprietary pool of universal 16S rRNA primers and species-specific primers were used to amplify a wide variety of species in clonal samples. The bacteria observed include Lactiplantibacillus, Limosilactobacillus, and Weissella. The population of Lactiplantibacillus in the cassava microflora increased with and without salt treatment, while Weissella, a new genus, was detected in 20 and 25% of salt-treated samples. Lactiplantibacillus and Weissella accounted for 32 and 68% and 60 and 40% of the bacterial populations detected at 20 and 25% salt treatment, respectively. A total of 17 strains and sequences were identified from the 30 isolates screened. Sequencing results classified the 30 isolates into four groups, of which 76.67% were Limosilactobacillus. Phylogenetic analysis showed that all 17 strains were divided into three clusters. These results show that high salt-mediated fermentation of cassava can trigger a shift in dominance in the bacterial community, changing the diversity of the microbial community.