In the present investigation we report the antibacterial activity of halistanol sulfate A isolated from the sponge Petromica ciocalyptoides, as well as of rodriguesines A and B isolated from the ascidian Didemnum sp., against the caries etiologic agent Streptococcus mutans. The transcription levels of S. mutans virulence genes gtfB, gtfC and gbpB, as well as of housekeeping genes groEL and 16S, were evaluated by sqRT-PCR analysis of S. mutans planktonic cells. There were no alterations in the expression levels of groEL and 16S after antimicrobial treatment with halistanol sulfate A and with rodriguesines A and B, but the expression of the genes gtfB, gtfC and gbpB was down-regulated. Halistanol sulfate A displayed the most potent antimicrobial effect against S. mutans, with inhibition of biofilm formation and reduction of biofilm-associated gene expression in planktonic cells. Halistanol sulfate A also inhibited the initial oral bacteria colonizers, such as Streptococcus sanguinis, but at much higher concentrations. The results obtained indicate that halistanol sulfate A may be considered a potential scaffold for drug development in Streptococcus mutans antibiofilm therapy, the main etiologic agent of human dental caries.