Lactic acid-producing bacteria (LABs) are known to have various beneficial properties for health. However, they are generally considered to have an adverse effect on teeth, since they produce acid. Nonetheless, milk and cheese containing specific LAB strains were recently found to have an inhibitory effect on dental caries in children, with an inhibitory activity towards the growth of Streptococcus mutans suggested as the responsible mechanism. Accordingly, the current study selected a probiotic candidate for oral health and studied its inhibitory mechanism against dental caries. Twenty-two LAB species belonging to eleven genuses were screened for promoting bone nodule formation using direct microscopic examination. Only one isolate, Weissella kimchii strain PL9001, increased the bone nodule formation significantly. The addition of W. kimchii strain PL9001 to bone cells prepared from mouse calvaria increased the bone nodule formation, calcium accumulation, and activity of alkaline phosphatase (the osteoblastic marker). Moreover, W. kimchii strain PL9001 inhibited the invasion of Streptococcus mutans into bone cells, and an organic extract of the culture supernatant of W. kimchii strain PL9001 inhibited the growth of Strep. mutans. Therefore, the results suggest that W. kimchii strain PL9001 can be used as a preventive measure against dental caries. This is the first time that a LAB has been shown to promote bone nodule formation and prevent the invasion of Strep. mutans into bone cells.