There is an increasing trend in the application of probiotics in aquaculture as an environment friendly alternative to antibiotics for the control and treatment of diseases. The microbiome of commercial aquaculture probiotics were evaluated using NGS to understand the microbial species composition vis-à-vis the label on the probiotic product. Bacteria belonging to 12 bacterial species stated on the labels of five probiotics were absent. The sequence reads of the microorganisms declared on the label ranged from 0.28-79 % for the probiotics tested while the rest were contaminants. The number of contaminant bacteria varied from 2 to 15 for the tested products. All products were found to have at least one bacterial species that were potentially pathogenic or of fecal origin. To our knowledge this is the first study that utilized the potential of NGS to assess the microbial quality of commercial aquaculture probiotics providing novel insights in understanding the microbial composition of probiotic products which are otherwise difficult to identify. It is proposed that probiotic products shall be approved for use in aquaculture after determining the performance efficiency by in vivo trails in farms, analysis of bacterial composition and concentration which shall be displayed on product labels.