Objectives: Earlier reports suggested that aggressive periodontitis is common in certain African populations and is associated with the JP2 clone of Aggregatibacter actinomycetemcomitans (Aa). There are few studies that investigated the type of microorganisms that colonize the subgingival sites in young subjects inflicted with a subcategory of aggressive periodontitis that is associated with the Aa-JP2 clone. Hence, the objective of this study was to characterize the subgingival microbiome of JP2 clone-associated aggressive periodontitis. Methods: The study subjects were drawn from a large survey among 14-18 years old schoolchildren in Morocco. The sample included 7 JP2-positive aggressive periodontitis subjects and 14 JP2-negative controls. The controls were selected to be either JP2-positive, JP2-negative (but Aa positive), or Aa-negative. Subgingival samples from these subjects were sequenced for the V1-V3 region (16S rRNA gene) on a Miseq platform. High-quality, non-chimeric merged reads were classified with our previously reported BLASTn-algorithm. Downstream analysis was performed with QIIME and LEfSe. Results: There were no significant differences between the groups in species richness. However, aggressive periodontitis subjects showed significantly lower alpha diversity. The microbiomes of aggressive periodontitis clustered distinctively from the controls. However, there was no significant separation between the subgroups of the control group. Species associated with health included Streptococcus spp., Haemophilus spp., Neisseria spp., Gemella spp., Rothia spp., Fusobacterium nucleatum subsp. polymorphum, Porphyromonas oral taxon 279, Veillonella parvula, Granulicatella adiacens and Lautropia mirabilis. Important periodontal pathogens, including Treponema spp., Fretibacterium spp. P. gingivalis and Tannerella forsythia were significantly enriched in aggressive periodontitis subjects. However, the taxa detected in high abundance and showed strongest association with aggressive periodontitis but not the controls were Pseudomonas oral taxon C61 and Enterobacter cloacae. Conclusions: The results suggest that several periodontal pathogens involved in chronic periodontitis also play a role in aggressive periodontitis. Future studies should investigate the role of Pseudomonas and Enterobacter spp. in the pathogenesis of aggressive periodontitis. / Oral Biology