Periodontitis is a chronic, inflammatory disease characterised by the destruction of the gums and bone supporting the teeth. It is associated with a build-up of subgingival plaque bacteria, specifically, Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia that correlate strongly with the onset and progression of the disease. The interaction between these bacteria has been documented, but the molecular mechanisms underlying the development of multi-species biofilms are poorly understood. Our study aims to provide detailed descriptions of the architecture of biofilms containing these species at all stages of their development using high-resolution imaging modalities. We have grown all three bacteria inside the flow cell system for 90 hrs, resulting in microcolonies about 200 µm thick. The dynamics and biogeography of the system will be explored by analysing it at several time points. Moreover, using cryo-electron tomography, we have recorded the molecular structures of individual bacteria in their native form. Interestingly, T. forsythia is decorated with a 2D crystalline surface (S-) layer composed of two glycoproteins, TfsA and TfsB. We were able to get a high-resolution structure of the S-layer revealing a unique structure consisting of three layers, 13 nm thick. The major densities in each layer form a diamond-shaped structure where the top and bottom layers are superimposed on each other whereas the middle layer is translated to form a connection between both layers. These S-layers contribute to the adhesion and invasion of cells, and they assist in bacterial co-aggregation. This study will aid in the understanding of the structure and ecology of bacterial biofilms in general, and more specifically subgingival plaque. The knowledge gained could be used in the future for designing treatments to interfere with the development of the biofilms that cause periodontitis.