IntroductionThe possible association between Candida carriage in children and childhood caries has not been elucidated in the Japanese population. This study aimed to investigate the prevalence, maternal relatedness, and genotypic distribution of Candida albicans in this population. Materials and methodsWe collected dental plaque samples from 55 mother-child pairs in the Caries group and 25 pairs in the caries-free (CF) group to analyze microbial data (carriage and viable counts), focusing on Streptococcus mutans and C. albicans. Clinically isolated 118 Candida strains were further evaluated using arbitrarily primed polymerase chain reaction. ResultsA higher C. albicans carriage rate was observed in the Caries pairs (25.5 % in children, 47.3 % in mothers) than in CF pairs (0 % in children, 24.0 % in mothers). The viable counts of S. mutans were significantly higher in the Caries group than in the CF group (p < 0.05). In addition, S. mutans counts positively correlated with C. albicans counts in the dental plaque of caries-affected children (r = 0.549). Almost all Candida-positive children (92.9 %) were diagnosed with severe early childhood caries, and 79.7 % of Candida isolates from the mother-child pairs were similar at the strain level. C. albicans genotype A was the most predominant (70.6 %) strain, followed by genotype D (17.6 %) in dental plaques from children in the Caries group. ConclusionsThe presence of C. albicans is a risk factor for childhood caries in a Japanese population. Our findings provide new insights into maternal-child oral health instructions based on microbial factors associated with dental caries.