The gingival sulcus contains a complex ecosystem that includes many uncultivated bacteria. Understanding the dynamics of this ecosystem in transitions between health and disease is important in advancing our understanding of the bacterial etiology of periodontitis. The objective of this longitudinal study was to examine the stability of bacterial colonization in the gingival crevice and to explore the relationship between shifts in microbial composition and changes in periodontal health status using a comprehensive, quantitative, cultureindependent approach. Subgingival plaque samples and periodontal data were collected from 24 subjects over 2 years. Baseline and 2-year plaque samples were analyzed using quantitative ribosomal 16S cloning and sequencing. Ten subjects remained periodontally healthy over 2 years, the periodontal health of seven subjects worsened, and seven subjects showed clinical improvement. Bacterial stability was greatest among healthy, clinically stable subjects and lowest for subjects whose periodontal status worsened (P ‫؍‬ 0.01). Higher numbers of species lost or gained were also observed for subjects whose clinical status changed (P ‫؍‬ 0.009). This provides evidence that a change in periodontal status is accompanied by shifts within the bacterial community. Based on these data, measures of microbial stability may be useful in clinical diagnosis and prognosis. Regarding individual species, increases in levels of the uncultivated phylotype Veillonella sp. oral clone X042, a gram-negative bacterium and the most common member of the subgingival bacterial community, were associated with periodontal health (P ‫؍‬ 0.04), suggesting that this is an important beneficial species. Filifactor alocis, a gram-positive anaerobe, was found at higher levels in subjects with disease (P ‫؍‬ 0.01).The gingival sulcus contains a complex ecosystem formed by resident and transient bacteria, and the critical role of bacteria in the etiology of chronic periodontitis is well established. The etiology is widely thought to be polymicrobial (16), but the role of individual species and their complex interactions with the host is not well understood. The earliest studies were conducted using open-ended cultivation methods. These were followed by a generation of studies employing molecular detection methods such as hybridization assays and PCR to target bacteria identified by cultivation. These less cumbersome methods allowed much larger scale studies to be carried out. The most recent advance has been cloning and sequencing of 16S rRNA genes. This approach has once again allowed an open-ended exploration of bacterial populations and has revealed the presence of many uncultivated species (18).