Early colonisation of oral surfaces by periodontal pathogens presents a significant risk factor for subsequent development of destructive disease affecting tissues that support the dentition. The aims of the present study were to establish the age-dependent relationship between sub-gingival profiles of 22 Prevotella species/phylotypes in children, adolescents and adults from an isolated Aboriginal community and, further, to use this information to identify Prevotella species that could serve as microbial risk indicators. DNA isolated from sub-gingival plaque samples (three healthy sites and three inflamed/diseased sites) from adults, adolescents and children was screened for Porphyromonas gingivalis load and 22 Prevotella species/phylotypes by species-specific PCR. A noticeable feature in adolescents was the marked increase in colonisation by P. gingivalis across all test sites. The mean number of Prevotella species/phylotypes colonising inflamed/diseased sub-gingival sites increased with age. Progressive partitioning of selected Prevotella species/phylotypes to healthy or inflamed/diseased sites was evident. Prevalence of Prevotella intermedia, Prevotella oral clone P4PB_24 and Prevotella oris increased significantly with age in diseased sites. Similarly, significant age-dependent increase in colonisation of healthy as well as inflamed/diseased sub-gingival sites was apparent for Prevotella oralis, Prevotella multiformis, Prevotella denticola, Prevotella strain P4P_53 and Prevotella oral clone BR014. Early colonisation of children by P. gingivalis, P. intermedia and Prevotella oral clone P4PB_24 provides indication of risk for subsequent development of periodontal disease. In the present study, the complexity of Prevotella species within gingival sites is explored as a basis for evaluating contribution of Prevotella species to disease.