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Background: Obstructive sleep apnoea (OSA) is a risk factor for cardiovascular disease. Alterations in the gut microbiome have been implicated in the development of cardiovascular disease and may potentially link OSA to its cardiovascular consequences. However, only one study to date has investigated gut microbiomes in adult patients with OSA. Methods: 19 patients with OSA and 20 non-OSA controls participated in the study. Following a diagnostic sleep study, blood was collected for metabolic profiling, and the subjects provided a stool sample for microbiome analysis. The gut microbiome was investigated using the 16S ribosomal RNA method. Results: Patients with OSA had a higher relative abundance of the <i>Proteobacteria</i> phylum (<i>p</i> = 0.03), <i>Gammaproteobacteria</i> class (<i>p</i> = 0.01), <i>Lactobacillae</i> family (<i>p</i> = 0.02), <i>Lactobacillus</i> (<i>p</i> = 0.03), and <i>Roseburia</i> genus (<i>p</i> = 0.03), and a lower abundance of the <i>Actinobacteria</i> phylum (<i>p</i> = 0.03). The abundance of <i>Proteobacteria</i>, <i>Gammaproteobacteria</i>, <i>Lactobacillae</i>, and <i>Lactobacillus</i> were related to disease severity and dyslipidaemia (all <i>p</i> < 0.05), whilst the abundance of <i>Proteobacteria</i> and <i>Gammaproteobacteria</i> was also related to hypertension and cardiovascular disease (all <i>p</i> < 0.05). However, following adjustment for relevant confounders only the association between OSA and <i>Actinobacteria</i> remained significant (<i>p</i> = 0.04). Conclusions: Obstructive sleep apnoea is associated with only subtle changes in gut microbiome. Further studies should investigate gut dysbiosis in OSA.