The microbial diversity of biofilms formed on the surfaces of amalgam, glass-ionomer cement, and resin composite was analyzed by denaturing gradient gel electrophoresis (DGGE). The V2-V3 region of salivary microbial 16S rDNA gene sequences of planktonic and biofilm bacteria, after 1 day and 1 week of incubation, was amplified by polymerase chain reaction (PCR) and analyzed by DGGE. The amounts of strongly adherent phylotypes after 1 day and 1 week on the three dental restorative materials were more than those on hydroxyapatite. Streptococcus salivarius was detected in both loosely adherent and strong adherent groups of all 1-day samples. At 1 week, the amounts of loosely adherent and strongly adherent phylotypes present on the three restorative materials ranked in this ascending order: glass-ionomer cement < resin composite < amalgam. Results of DGGE analysis suggested that glass-ionomer cement was the best material of choice in terms of suppressing bacterial phylotypes in biofilms.