Abstract Objectives The aim of this study were to measurably detect Bifidobacterium and Scardovia wiggsiae in plaque from severe early childhood caries (S-ECC) and caries-free children and to analyze the interrelation between these bacteria and clinical caries presentation and caries-related factors assessed by questionnaire. Materials and Methods One-hundred forty supra gingiva plaque samples from children aged between 2 and 5 years were used in this study. There were 70 children in each group. Recorded plaque index, modified gingival index, and decay, missing, and filled tooth (dmft) scores. Parents' attitudes, child's oral hygiene, and diet were assessed by questionnaire. DNA was extracted from plaque samples and quantitative real-time polymerase chain reaction using fluorescent dye was performed. Results Plaque (p < 0.001) and modified gingival indices (p < 0.001) in the S-ECC group were higher than in the caries-free group. Prevalence of Bifidobacterium (p = 0.004) and S. wiggsiae (p < 0.001) in the S-ECC group was higher than in the caries-free group. The numbers of total bacteria (p = 0.003), Bifidobacterium (p < 0.001), and proportion of Bifidobacterium to total bacteria (p < 0.001) were higher in the S-ECC group. Detections of both bacteria, Bifidobacterium + S. wiggsiae (p < 0.001), were higher in the S-ECC group than in the caries-free group. In the S-ECC group, dmft scores (p < 0.001; p = 0.024) and the modified gingiva index (p = 0.004; p = 0.002) were higher in the presence of Bifidobacterium and S. wiggsiae, respectively. In the S-ECC group, the dmft scores (p = 0.005) and modified gingiva index (p = 0.004) were higher in the presence of both Bifidobacterium + S. wiggsiae. There were positive correlations between the Bifidobacterium level (p = 0.003), the proportion of Bifidobacterium to total bacteria (p = 0.017), and S-ECC. The level of Bifidobacterium (p < 0.001) and ratio of Bifidobacterium to total bacteria (p < 0.001) were correlated with the dmft score and modified gingival index in the S-ECC group. From the questionnaire, S-ECC were associated with major caregiver (p = 0.002), parent education levels (p = 0.02), prolonged bottle-feeding (>18 months) (p = 0.015), night-time feeding (p < 0.001), eating cariogenic snacks (p = 0.019), and frequency of dental visits (p = 0.003). Conclusions Levels of total bacteria, Bifidobacterium, S. wiggsiae and plaque, and the modified gingival indices were higher in the S-ECC group. Factors associated with S-ECC included the major caregiver, parent education levels, feeding patterns, cariogenic snacks consumption, and frequency of dental visits.