Oral Diseases (2012) 18, 595–601 Objective:  The purpose of this study was to determine the bacterial profiles in saliva of the isolated children for studying caries etiology. Materials and methods:  Samples were collected from isolated children from 6 to 8 years old including 20 caries‐free (dmfs = 0) (healthy) and 30 caries‐active individuals (dmfs > 8) (patients). 16S rRNA genes were amplified by PCR from bacterial DNA of saliva sample and labeled via incorporation of Cy3‐dCTP in second nested PCR. After hybridization of labeled amplicons on HOMIM, the microarray slides were scanned and original data acquired from professional software. Results:  Collectively, 94 bacterial species or clusters representing six bacterial phyla and 30 genera were detected. A higher bacterial diversity was observed in patients than in healthy samples. Statistical analyses revealed eight species or clusters were detected more frequently in diseased patients than in healthy samples, while six different species were detected more frequently in healthy as compared to diseased patients. Conclusion:  The diversity of microbe within saliva derived from isolated population increased in caries‐active status, and there are some bacteria in salivary flora can be as candidate biomarkers for caries prognosis in mixed dentition. The imbalances in the resident microflora may be the ultimate mechanism of dental caries.