High-throughput sequencing technology combined with plate colony counting method was used to detect and analyze the microflora of water kefir and its starter water kefir granules. Probiotics were screened from naturally fermented water kefir and water kefir granules, and the selected probiotics were identified by individual and population morphological observation, physiological and biochemical experiments and 16S rDNA sequence analysis. The results showed that lactic acid bacteria were the dominant bacteria in the two samples; whether it is water kefir or water kefir grain, Firmicutes and Proteus are the dominant bacteria, Lactobacillus and Acetobacter are the dominant bacteria, The bacterial diversity and richness of water kefir granules were higher than those of water kefir；A total of 7 strains of lactic acid bacteria with potential probiotics of acid and bile resistant salts were screened, and the identification results were four strains of Lactobacillus fermentum, one strain of Lactobacillus paracasei, one strain of Lactobacillus harbinensis and one strain of Lactobacillus rubrum were identified and named Lactobacillus fermentum cc4、Lactobacillus fermentum cc8、Lactobacillus fermentum cc9、Lactobacillus fermentum cc22、Lactobacillus paracasei cc1、Lactobacillus harbinensis cc5、Lactobacillus satsumensis cc12.