Background: This study compares the changes to the subgingival microbiota of individuals with “refractory” periodontitis (RP) or treatable periodontitis (good responders GR) before and after periodontal therapy by using the Human Oral Microbe Identification Microarray (HOMIM) analysis. Methods: Individuals with chronic periodontitis were classified as RP (n = 17) based on mean attachment loss (AL) and/or >3 sites with AL ≥2.5 mm after scaling and root planing, surgery, and systemically administered amoxicillin and metronidazole or as GR (n = 30) based on mean attachment gain and no sites with AL ≥2.5 mm after treatment. Subgingival plaque samples were taken at baseline and 15 months after treatment and analyzed for the presence of 300 species by HOMIM analysis. Significant differences in taxa before and post‐therapy were sought using the Wilcoxon test. Results: The majority of species evaluated decreased in prevalence in both groups after treatment; however, only a small subset of organisms was significantly affected. Species that increased or persisted in high frequency in RP but were significantly reduced in GR included Bacteroidetes sp., Porphyromonas endodontalis, Porphyromonas gingivalis, Prevotella spp., Tannerella forsythia, Dialister spp., Selenomonas spp., Catonella morbi, Eubacterium spp., Filifactor alocis, Parvimonas micra, Peptostreptococcus sp. OT113, Fusobacterium sp. OT203, Pseudoramibacter alactolyticus, Streptococcus intermedius or Streptococcus constellatus, and Shuttlesworthia satelles. In contrast, Capnocytophaga sputigena, Cardiobacterium hominis, Gemella haemolysans, Haemophilus parainfluenzae, Kingella oralis, Lautropia mirabilis, Neisseria elongata, Rothia dentocariosa, Streptococcus australis, and Veillonella spp. were more associated with therapeutic success. Conclusion: Persistence of putative and novel periodontal pathogens, as well as low prevalence of beneficial species was associated with chronic refractory periodontitis.