The purpose of the present study was to obtain diverse profiles of Prevotella species associated with gingival sites in an isolated Aboriginal and an urban community by phylogenetic analysis and to establish patterns of association of identified Prevotella species in gingival sites. Species/phylotypes identified from the phylogenetic analysis of near full-length Bacteroidetes 16S rRNA gene sequences cloned from subgingival plaque samples obtained from an Aboriginal community were compared with those from an ethnically diverse urban metropolitan population suffering from periodontal disease. Specific primer sets were designed and validated for 22 distinct Prevotella species from the 24 species/phylotypes identified from both populations. Within the isolated Aboriginal community, gingival sites in adults were colonised by a mean of 15 different Prevotella species. Prevotella sp. oral clone P4PB24, Prevotella intermedia, Prevotella oralis, Prevotella denticola and Prevotella sp. strain P4P62 had the highest association with increasing probing depth in diseased sites (p < 0.05). P. intermedia and Prevotella sp. oral clone P4PB24, the Prevotella species significantly associated with increasing probing depth in diseased gingival sites and also strongly associated with P. gingivalis load (p < 0.05) in diseased gingival sites, showed significant correlation for co-colonisation (r = 0.6). Prevotella sp. oral clone B31FD, showing strong association with P. gingivalis load (p < 0.05) in diseased gingival sites, showed no significant correlation for co-colonisation with any other Prevotella species. This study provides a comprehensive analysis of Prevotella species associated with gingival sites for the informative evaluation of the epidemiology of infection by this genus.