This study reports the detection and identification of four commonly occurring dental bacteria including Prophyromonas gingivalis, Bacteroides forsythes, Actinobacillus actinomycetenicomitans and Prevotella intermedia using PCR amplification with 16S rRNA sequence-specific primers. The phylogenetic relationship among these bacteria was also studied after retrieving 16S rRNA gene sequences from the GenBank nucleotide database. There were positive amplifications for Actinobacillus actinomycetenicomitans in 6 out of 8 samples followed by Prophyromonas gingivalis (5/8) and Bacteroides forsythes (3/8) whereas only one sample was positive for Prevotella intermedia. Multiple sequence alignment showed a large number of variable sites (547 out of post-alignment 1510 sites) while the average frequencies of conserved sequences among the species were 60.9%. The phylogenetic tree clearly differentiated Actinobacillus actinomycetenicomitans and Prevotella intermedia from Prophyromonas gingivalis and Bacteroides forsythes, the later two species belong to the same family (but different genera) and appeared as a separate clade. The hierarchical flow of the tree clearly showed the discriminatory power of 16S rRNA marker from phylum to genus level. In conclusion, PCR amplification using 16S rRNA sequence-specific primers provides a sensitive and specific method for identification of dental bacteria. This method does not require any culturing or DNA extraction hence is more simple and time saving. Post-amplification sequencing of 16S rRNA provides a reliable tool for phylogenetic and molecular diversity analyses.