To investigate the effect of bacteria on diatoms at the community level, sediment samples from an intertidal tropical environment were treated with penicillin (a Beta-lactam antibiotic that can affect diatoms only through bacteria). Streptomycin (an aminoglycoside) and chloramphenicol, antibiotics that can potentially affect protein synthesis in diatom organelles and photosynthesis, were also used for comparison. The changes in diatom community structure and the resistant and tolerant bacterial fractions were analyzed through microscopy, culture techniques and denaturing gradient gel electrophoresis. The reduction in bacterial abundance when treated with penicillin resulted in suppression of Amphora coffeaeformis, a dominant diatom in the study area. The bacterial community preferred the ‘tolerance’ strategy over ‘resistance’ in response to treatment with penicillin; these changes in bacterial dynamics were probably linked to concurrent changes in diatom community structure. The observations with penicillin differed from those with streptomycin that did not seem to significantly affect diatoms, and chloramphenicol, which consistently inhibited diatoms. Overall, the results of this study highlight the significance of bacteria in structuring benthic diatom communities and call for the inclusion of the ‘antibiotics’ approach in studies addressing diatom-bacterial interactions at the community level.