AIMS To test the effect of 0·4% stannous fluoride (SnF2 ) glycerine-based gels on specific portions of the bacterial community in both a clinical observational study and in vitro multispecies plaque-derived (MSPD) biofilm model. METHODS AND RESULTS Potential changes to specific portions of the bacterial community were determined through the Human Oral Microbial Identification Microarray (HOMIM). Both the observational clinical study and the biofilm model showed that short-term use of 0·4% SnF2 gel has little effect on the bacterial community depicted by hierarchical cluster analysis. The amount of plaque accumulation on a subject's teeth, which was measured by plaque index scores, failed to show statistical significant changes over the two baselines or after treatment (P = 0·9928). The in vitro results were similar when examining the effect of 0·4% SnF2 gels on biofilm adherence through a crystal violet assay (P = 0·1157). CONCLUSIONS The bacteria within the dental biofilms showed resilience in maintaining the overall community diversity after exposure to 0·4% SnF2 topical gels. SIGNIFICANCE AND IMPACT OF THE STUDY The study supports that the immediate benefits of using 0·4% SnF2 gels in children may be strictly from fluoride ions inhibiting tooth demineralization rather than delivering substantial antimicrobial effects.