Not only several selected bacteria but also oral microbiota are closely related to the initiation and progression of early childhood caries(ECC). Oral microbes and the host are in a dynamic balance in normal physiological conditions; however, this varying balance ultimately determines oral infectious disease. Microbiota varies between individual, plaque, and saliva. The microbial diversity of caries-free children is higher than that of severe ECC(SECC) children, and it decreases before caries appears, that is, the caries may be associated with the decrease of microbial diversity. Microbiota composition of SECC children significantly changes post-therapy. Probiotics can decrease the number of cariogenic bacteria and prevalence rate of caries. Learning more about children’s oral microbiota will provide higher predictability of ECC development and lead to the implementation of targeted early intervention. This review focuses on recent microbiological findings about ECC-associated microbiota.