In this study, longitudinal changes in the composition of the subgingival microbiota of children between the ages of 11 and 14 and their association with changes of clinical parameters describing gingival health were investigated. During 4 years, subgingival microbial samples were taken in 22 boys and 20 girls 10 times. At the same time the gingival bleeding tendency was recorded by the Papillary Bleeding Index (PBI). A total of 840 samples was evaluated using darkfield microscopy and anaerobic culturing on non-selective and selective media. Children, who developed a marked and sustained increase in mean PBI scores (n = 21), had higher frequencies and mean proportions of spirochetes and Eikenella corrodens than children without pronounced puberty gingivitis (p less than = 0.05). The mean proportion of Actinomyces viscosus was also higher in these children (p less than = 0.05). Among the species discriminated, only Capnocytophaga sp. were found at a higher rate in samples taken immediately before a rise of PBI (p less than = 0.05). The detection frequencies of black-pigmented Bacteroides (particularly B. intermedius) increased later, and were significantly elevated after the establishment of a high bleeding tendency (p less than = 0.05). These findings implicate Capnocytophaga sp. in the initiation of puberty gingivitis, whereas the increased presence of Bacteroides may reflect a change in the subgingival environment secondary to increased bleeding.