Fibromyalgia syndrome (FMS) is one of the most frequent forms of chronic widespread pain, with a reported prevalence of 3-10% in the adult population. Clinical presentation of the typical pain and the presence of associated somatic and psychological symptoms form the basis of the diagnosis. FMS is associated with nervous system dysfunction and neurotransmitters act as targets of a number of drugs approved for fibromyalgia. However, although the underlying mechanisms in FMS are not yet known precisely, many hypotheses have been put forward. Considering the relation between fibromyalgia and irritable bowel syndrome (IBS), altered gut microbiome could be associated with fibromyalgia. In this study, it was aimed to investigate the variation of intestinal microbiome levels in patients with FMS compared to healthy controls. For the investigation of the microbiome, fecal samples were collected from a cohort of 54 patients with FMS and 36 healthy individuals. Those with any mental and/or physical illness in the control group were excluded from the study. The FMS patient group was determined according to the "American College of Rheumatology (ACR)" 2010 diagnostic criteria. The fecal samples were stored at -80 degrees C until use and were thawed on ice; for each extraction, 0.3 g of faeces were weighed. Extraction of DNA was carried out with commercial kit according to the manufacturer's recommendations. Samples were compared using 16S rRNA gene amplification with specific primers of Bacteroidetes, Firmicutes, Enterobacter, Lactobacillus, Streptococcus and Bifidobacterium by the real-time PCR method. According to our results, while the increase of Bacteroidetes and Bifidobacterium was statistically significant (p< 0.05), Firmicutes decreased (p< 0.001) in the patient group. No statistically significant results were found for Enterobacter, Streptococcus and Lactobacillus (p> 0.05). When the relationship between bacteria was evaluated, a high statistically significance and negative correlation was found between Bacteroidetes and the percentage of Firmicutes (r= -0.778, p< 0.001),while a moderate statistical significance and positive correlation was observed between the percentage of Enterobacter and Bifidobacterium (r= 0.460, p= 0.005). The results suggest that the gut microbiota may play a role in fibromyalgia. The balance of Firmicutes and Bacteroidetes phyla in the gut is known to have important effects on intestinal homeostasis. In summary, it is clear that large-scale further research in larger cohorts will be effective in understanding the relationship between the gut microbiome and FMS and evaluating possible treatment options.