Oral lactobacilli are members of a group of bacteria implicated in caries progression, although information regarding their transmission, colonization, and caries-associated species is not well established. This study isolated oral lactobacilli from a group of children with primary dentition for determination of Lactobacillus prevalence, detection of Streptococcus mutans, a major pathogen of caries initiation, and dental caries status of the children. Species of Lactobacillus isolates were determined from examination of 16S rDNA sequences. Subsequently, the most prevalent species was evaluated for involvement in caries status, and binding ability to type I collagen of all Lactobacillus isolates was determined in association with caries status. Multilocus sequence typing (MLST) of eleven loci was carried out to study strains of the predominant Lactobacillus sp. The detection of oral lactobacilli together with S. mutans was significantly associated with the highest dental caries indices, but there was no involvement of collagen-binding properties of Lactobacillus isolates in caries status. Lactobacillus fermentum was the most prevalent, and its presence was related to high scores of caries indices. MLST analysis of L. fermentum population could not specify a particular clone associated with caries status, but revealed sharing of identical L. fermentum strains among children in the same classrooms. Taken together, the data contributed useful information on the role of oral lactobacilli, in particular L. fermentum in dental caries.