Hidradenitis suppurativa (HS) is a chronic inflammatory disorder of the pilosebaceous unit of the intertriginous body areas. Recent findings have suggested the association between periodontitis and HS. This investigation aimed to characterize and compare the composition of subgingival microbiome between HS, periodontitis, and control patients. The nine crucial perio-pathogenic species and total bacteria were analyzed using RT-PCR based tests in samples collected from 30 patients with periodontitis, 30 patients with HS and 30 controls. Patients with HS were excluded if they had periodontitis and patients with periodontitis were excluded if they had HS. The mean total bacteria count was significantly higher in HS and periodontitis samples than in control samples (p < 0.05). The majority of perio-pathogens tested were more frequently detected in HS and periodontitis groups than among controls. Treponema denticola was the most common pathogen in individuals with HS (70%) and periodontitis (86.7%), while among controls Capnocytophyga gingivalis was the most frequently detected isolate (33.2%). The results of the present investigation demonstrated that HS and periodontitis patients share some similarities in their subgingival microbiome composition.