The type IX secretion system (T9SS) has been recently discovered and is specific to Bacteroidetes species. Porphyromonas gingivalis, a keystone pathogen for periodontal disease, utilizes the T9SS to transport many proteins including the gingipain virulence factors across the outer membrane and attach them to the cell surface. The proteins transported by the T9SS have a conserved C-terminal domain (CTD), which is the signal for translocation across the outer membrane via the T9SS. At least 14 proteins, namely; Sov, PorK, PorL, PorM, PorN, PorP, PorQ, PorT, PorU, PorV, PorW, PorZ, PG1058 and PG0534, have been identified as components of the T9SS. However, the overall organisation and the dynamic interactions between these proteins have not been elucidated fully. In this study, we analysed P. gingivalis wild-type and P. gingivalis T9SS mutants using 1-D Blue Native Page (BN-PAGE) proteomics to identify a comprehensive interactome of the T9SS. The recent advances in mass spectrometry has enabled us to identify needles in a haystack. We show for the first time that the T9SS is organised as four sub-complexes and identify the components in each sub-complex. Sub-complex (i) PorK, PorL, PorM, PorN and PorT, (ii) Sov and PorW, (iii) PorP and PG1058 and (iv) PorU, PorV, PorQ and PorZ. We have validated these interactions using co-immunoprecipitation and chemical cross-linking. Further analysis of the P. gingivalis T9SS mutants have shed light on the potential role of the sub-complex PorP-PG1058 as the one that recruits T9SS substrates from the translocation channel and passes them on to PorV. PorV has been identified as a shuttle protein that transports the T9SS substrates to sub-complex (iv) which we have named the attachment complex as it is involved in the attachment of the translocated proteins to the bacterial cell surface. In summary, this is the first report showing a comprehensive interactome of the T9SS.