OBJECTIVES: To describe the taxonomy of the microbiota in crevicular fluid of primary Sjögren's syndrome (pSS) patients, and evaluate its association with clinical/serological variables, and oral quality of life. METHODS: Observational study that included 48 pSS without diabetes mellitus, no active neoplasia, no antibiotic use in the previous two weeks, and no current active infection. We registered demographics, oral/ocular sicca symptoms, parotid enlargement and anti-Ro/La serology. We assessed the non-stimulated whole salivary flow (NSWSF), the EULAR Sjögren's Syndrome Patient Reported Index (ESSPRI), and the Xerostomia-related Quality of Life Scale (XeQoLS). Two periodontists determined the presence of periodontal disease and collected crevicular fluid from 6 teeth using filter paper. Samples were frozen at -86°C until processing. We included 17 sex- and age-matched control subjects. Bacterial DNA was extracted from the crevicular fluid sample using a commercial kit. 16SrRNA V3-V4 region was sequenced using reversible adaptor technology. Sequences were pre-processed and analysed using QIIME2 and phyloseq software programs. Functionality profiles were predicted using the Tax4Fun2 package. RESULTS: PSS patients had more bacteria of the genera Prevotella, Streptococcus, Veillonella, Fusobacterium, and Leptotrichia and fewer bacteria of the genus Selenomonas than controls. The pSS microbiota contained more genes encoding accessory secretory proteins. Microbiota also differed between patients with anti-Ro/La status, parotid gland enlargement, and periodontal disease severity, but did not correlate with NSWSF and XeQoLS. CONCLUSIONS: The crevicular fluid microbiota of pSS patients and controls differed significantly, even in SSP patients depending on their serology, parotid gland enlargement, and periodontal disease status.