Background: Probiotics are widely accepted functional foods for general well-being and a healthy lifestyle. A robust approach to evaluate the bio-similarities between marketed probiotics still needs to be developed. Aim: We aimed to define an approach that uses time-tested methods to evaluate pro-biosimilarity between different marketed probiotics. Methods: A total of five different Bacillus clausii formulations were compared with the international reference standard Enterogermina. The spore quantity and microbial purity of the samples were estimated. The antibiotic resistance strains in oral suspension samples were isolated and subjected to molecular characterization by 16S rRNA sequencing. The antibiotic susceptibility test was performed using commercially available antibiotics. The pH and transmittance of the samples were measured. Results: BifilacClausi had the highest, while Entromax had the lowest density of quality spores. None of the products had contaminant pathogenic microorganisms. Based on 16s rRNA sequencing, four strains from BifilacClausi and Enterogermina and one strain from other samples were identified. The identity of the strains from BifilacClausi matched those of Enterogermina. BifilacClausi and Enterogermina were resistant to the ten antibiotics tested. Conclusions: Among the different Indian brands of Bacillus clausii, only BifilacClausi was found to be a pro-biosimilar to the international reference standard, Enterogermina.