Chronic widespread musculoskeletal pain (CWP) is a characteristic symptom of fibromyalgia, which has been shown to be associated with an altered gut microbiome. Microbiome studies to date have not examined the milder CWP phenotype specifically nor have they explored the role of raised BMI. The aim of this study was to investigate whether the microbiome is abnormal in CWP.CWP was assessed using a standardized screening questionnaire in female volunteers from the TwinsUK cohort including 113 CWP cases and 1623 controls. The stool microbiome was characterised using 16S rRNA amplicon sequencing and amplicon sequence variants (ASVs), and associations with CWP examined using linear mixed-effects models adjusting for BMI, age, diet, family relatedness and technical factors.Alpha diversity was significantly lower in CWP cases than controls (Mann-Whitney test, p-values 2.3e-04 and 1.2e-02, respectively). The species Coprococcus comes was significantly depleted in CWP cases (p.adj = 3.04e-03). A genome-wide association study (GWAS) performed for C. comes in TwinsUK followed by meta-analysis with three Dutch cohorts (total n = 3521) resulted in nine suggestive regions, with the most convincing on chromosome 4 near the TRAM1L1 gene (rs76957229, p= 7.4e-8). A Mendelian randomisation study based on the results of the GWAS did not support a causal role for C. comes on the development of CWP.We have demonstrated reduced diversity in the microbiome in CWP, indicating an involvement of the gut microbiota in CWP; prospectively the microbiome may offer therapeutic opportunities for this condition.