Streptococcus mutans, known to be an aetiological agent of dental caries, is occasionally isolated from patients with infective endocarditis (IE). S. mutans strains with a defect in all three types of glucosyltransferase (GTF) obtained from an infected heart valve extirpated from an IE patient have been reported previously. In this study, molecular analyses of strains detected in heart valve (strain V1) and dental plaque (strain P1) samples taken from the same patient were performed. Complete nucleotide alignments of the gtfB, gtfC and gtfD regions in strains V1 and P1, as well as in the reference strain MT8148, were determined, which revealed the existence of alignments with a high similarity to erythromycin- and spectinomycin-resistance genes in the middle of the gtfB-gtfC and gtfD genes, respectively, of V1. Strain V1 also showed a higher MIC for these two antibiotics compared with strain P1. Next, primers to detect the specific sequences of the antibiotic-resistance genes in strain V1 were constructed and PCR amplification was performed with template DNA from dental plaque and infected valve tissue samples taken from the patient. Attenuated expression of GTFs in V1 caused a significantly lower susceptibility to phagocytosis by human polymorphonuclear leukocytes compared with the reference strain. These results suggest that the blood isolate V1 found in the oral cavity invaded and survived in the bloodstream for a long duration and that this was related to its virulence in IE in our patient.