Introduction Nonalcoholic fatty liver disease (NAFLD), a condition with upward trend and worldwide distribution is often associated with obstructive sleep apnea (OSA). The aim of the present study was to highlight the clinical and gut microbiota particularities in patients with NAFLD and OSA.  Patients and Methods.100 patients, 58 females, 42 males, age range 29-74 years, with NAFLD were evenly included in this cross-sectional study, depending on the presence or absence of OSA. Thoroughly clinical examination with neck and waist assessment, body mass index (BMI), blood pressure measurement, lab work-ups, fatty liver index (FLI), liver abdominal duplex ultrasonography and elastography, Carotid Eco Doppler, ECG, echocardiography, thorax plain radiology, polysomnography, as well as stool with dysbiosis severity assessment. Next generation 16S ribosomal RNA stool sequencing was performed in dysbiotic patients. Results: Significant differences in favor of patients with OSA were noted related to age (57.7±5.85 vs. 53.45±5.05, p=0.073), NASH score (0.28±0.16vs. 0.19±0.08, p=0.0001), FLI (63.48±7.23 vs. 52.23±0.65, p<0.0001),BMI (33.03±2.51vs. 29.5±3.21,p p<0.0001),gut dysbiosis (2.31±0.58vs1.83±0.51,p<0.0001) and various comorbidities: diabetes mellitus (30% vs.12%, p-0.0279), dyslipidemia (76%vs.56%,p=0.0357), atherosclerotic plaques (60%vs.40%, p-0.0466), diastolic heart insufficiency (54%vs.34%,p=0.045),, pulmonary hypertension (36%vs.6%,p=0.0002). No significant differences were noted related to hypertension (58%vs.40%, p=0.0732) and chronic kidney disease (40%vs.22%p=0.0528). Close correlations between NASH scores and OSA severity, as well as between NASH and dysbiosis severity were observed. Decrease of stool biodiversity, abundance of enterotypes 1 and 2, alterations of Firmicutes/Bacteroidetes ratio and modifications of functional microbiota, such as Faecalibacterium prausnitzii, and Akkermansia muciniphila as well as Prevotella spp., were frequently noted in patients with NAFLD and OSA. Conclusions:  Patients with NAFLD and OSA displayed older age, more severe liver damage, increased average of BMI and FLI, as well as numerous cardio- vascular and metabolic issues. Alterations of the gut microbiota biodiversity, decreased mucosa protective and mucin degrading bacteria represent an additional burden, multiplying the risk of bad outcome. The assessment of microbiota changes may provide valuable keys for customized interventions to improve the outcomes.