Actinomyces are Gram-positive pleomorphic rods (GPPR) which form a large proportion of the oral microflora of all mammals. They have been implicated in root caries, although their role in dental caries initiation and progression is not well-understood. Many studies have focused on Actinomyces naeslundii, but few reports have documented other members of the GPPR. Therefore, we investigated the GPPRs isolated from infected dentin of active root caries lesions (n = 9) to determine which species were the most frequently isolated. The GPPR were isolated under both aerobic and anaerobic conditions and identified by biochemical and physiological tests to the species level according to the new taxonomy. Of 654 GPPR isolates investigated, 607 were identified as belonging to the genus Actinomyces. Of these, 242 were identified as A. israelii, 225 as A. gerencseriae, 109 as A. naeslundii, 15 as A. odontolyticus, and 13 as A. georgiae. Individual strains of A. israelii (n = 56) and A. gerencseriae (n = 46) were also investigated at the DNA level by means of Repetitive Extragenic Palindromic polymerase chain-reactions (REP-PCR) for the study of clonal diversity. Although only a small number of isolates was investigated, REP-PCR showed that the genotypes of both A. gerencseriae and A. israelii populations were heterogeneous within individual root caries lesions. A. gerencseriae and A. israelii strains from the same lesions did not share the same REP-PCR patterns, showing the robustness of the identification scheme. A significantly greater proportion of A. gerencseriae was isolated from the aerobic plates (p < 0.05), while the proportion of A. israelii was significantly (p < 0.05) greater from anaerobic plates. The role of individual Actinomyces spp. in the root caries process remains unclear, since various populations of GPPRs were isolated from individual active root caries lesions.