This study aims to assess differences in biofilm bacterial composition between patients with low and high caries. Patients without a medical problem and with no history of antibiotic use, mouth wash or fluoride application in the previous 3 months were recruited. Caries was recorded at cavitation level; score was calculated by a national mean (dmft of 4.8 and DMFT of 2.7). Pooled biofilm samples were collected from mesial, distal, buccal, lingual, and occlusal surfaces. Based on caries experience, individuals were classified into low and high caries and both groups were compared regarding bacteria identified using
16S rRNA
gene sequencing, and molecular phylogenetic analysis of the isolates was performed. A total of twenty seven randomly selected samples with low (
n
= 13) and high (
n
= 14) caries. Identification of oral bacteria was performed using
16S rRNA
sequence,
Rothia mucilaginosa
and
R. aeria
were identified in low caries individuals, while
R. dentocariosa
was detected in high caries individuals. Two
Streptococcus
spp. were identified only in low caries
S. salivarius
and
S. gordonii
whereas
S. sanguinis, S. mitis, S. sinensis, S. rubneri, S. vestibularis, S. cristatus
and
S. massiliensis
were identified only in individuals with high caries. This study revealed the absence of
R. mucilaginosa
in the high caries subjects and its coexistence with the low caries subjects.
Streptococcus mutans
was insignificant contributor of caries among samples, while,
Streptococcus sanguinis
was the main constituent of high caries Saudi patients.