Streptococcus mutans is a gram-positive facultative anaerobic that belongs to the mutans streptococci group and is considered to be an important pathogen associated with human dental caries. 106 S. mutans isolates were isolated from 140 clinical samples. The 106 isolates comprised 56 isolates from soft caries lesion, 50 isolates from dental plaque samples, the latter included 30 isolates from plaque of caries active and 20 isolates from plaque of caries-free. The isolates showed sticky and rough colonies on TYCSB media. Isolates produced alpha hemolysis on blood agar. Isolates were catalase-negative and able to ferment mannitol, sorbitol, inulin and sucrose. The identification of S. mutans was confirmed by the detection of the S. mutans-specific glucosyltransferase gene (gtfB) using PCR specific primers for S. mutans gtfB gene. Isolates were tested for their sensitivity to diverse antimicrobial agents. It was found that 99% of the isolates were sensitive to ofloxacin and levofloxacin and 88.5% of isolates was sensitive to chloramphenicol, however, 80.2%, 75.5% and 65% of the isolates were resistant to ceftriaxone, cefotaxime and erythromycin, respectively. It was recorded that 90.5% and 85.8% of the isolates were sensitive to linezolid and tetracycline, respectively, and were highly resistant to clindamycin with a frequency of 95.3%. Based on the statistical analysis using the chi-square test, there was a significant difference in antimicrobial susceptibility profiles among the three groups with higher frequencies among soft caries lesion isolates (P < 0.0001). Therefore, the extensive use of antimicrobials in treatment and prophylaxis in dental caries must be controlled.