Background: Severe early childhood caries is a rapidly progressing form of dental caries that affects young children and is strongly associated with microbial factors. Understanding the salivary microbial profile in children with S-ECC is critical for developing targeted preventive and therapeutic strategies. Objectives: This study aims to analyze the presence of S. mutans, S. sobrinus and S. wiggsiae in saliva samples obtained from children with severe-ECC. Materials and Methods: This cross-sectional study included children aged 3 to 5 years diagnosed with S-ECC, from January 2020 to May 2020. Ethical approval was obtained from Marmara University Clinical Research Ethical Committee and written informed consent was obtained from parents. Oral examinations were conducted under WHO criteria (1997), recording dmft and ICDAS II scores alongside demographic and feeding habits. Unstimulated saliva samples were collected using a saliva ejector and stored for analysis. q-PCR was performed to detect saliva S. mutans, S. wiggsiae, and S. sobrinus using species-specific 16S rRNA primers. Results: A total of 54 children (40.7% female, 59.3% male) with a mean age of 4.2 ± 0.8 years and a mean dmft score of 13.2 ± 3.2 participated in the study. All children were classified within the ICDAS code 5–6 group. Saliva samples from 52 children were analyzed via qPCR, revealing S. mutans in 96.2%, S. wiggsiae in 67.3%, and S. sobrinus in 26.9%. Co-detection rates were 66.0% for S. mutans and S. wiggsiae, 26.9% for S. mutans and S. sobrinus, and 9.6% for S. sobrinus and S. wiggsiae. No significant associations were found between S. mutans levels and the duration of bottle feeding or breastfeeding (p=0.207 and p=0.184, respectively). Conclusions: This study suggests that S. mutans and S. wiggsiae are prevalent in children with S-ECC, but feeding practices showed no significant impact on the quantity of S. mutans.