Palatine tonsils are the only air-contacted lymphoid organs that constantly engage in crosstalk with commensal microorganisms and serve as the first handling sites against microbial antigens. While tonsil inflammations have been implicated in various autoimmune diseases, including rheumatoid arthritis (RA), the precise role of tonsillar microbiota in autoimmune pathogenesis remains inadequately characterized. In this study, we profiled the tonsillar microbiota and identified a notable dysbiosis in patients with RA, particularly within the
Streptococcus
genus. Specifically, patients with RA exhibited an enrichment of pathogenic
Streptococcus
species, including
S
.
pyogenes
,
S
.
dysgalactiae
, and
S
.
agalactiae
. Colonization with these bacteria significantly exacerbated arthritis severity and increased autoimmune responses in collagen-induced arthritis (CIA). Furthermore, immunization with peptides derived from these pathogenic
Streptococcus
species directly induced experimental arthritis. Conversely, patients with RA demonstrated a marked deficiency in commensal
Streptococcus
members, notably
S
.
salivarius
. Treatment of CIA mice with
S
.
salivarius
attenuated the progression of arthritis and downregulated autoimmune responses. These findings highlight a pathogenic link of tonsillar microbiota with RA, shedding light on their contribution to autoimmunity.