The mycobiotic component of the microbiota comprises an integral, yet under-researched, part of the gastrointestinal tract. Here, we present a preliminary study of the possible contribution of gut mycobiota to sub-clinical atherosclerosis in a well-characterised group of obese and non-obese subjects in association with the Framingham Risk Score (FRS) and carotid intima-media thickness (cIMT). From all taxa identified, the relative abundance of the phylumZygomycota, comprising the familyMucoraceaeand genusMucor, was negatively associated with cIMT and this association remained significant after controlling for false discovery rate. Obese subjects with detectableMucorspp. had a similar cardiovascular risk profile as non-obese subjects. Interestingly, the relative abundance ofMucor racemosuswas negatively associated both with FRS and cIMT. Partial least square discriminant analyses modelling, evaluating the potential relevance of gut mycobiota in patients stratified by mean values of cIMT, showed that even a 1 component model had a high accuracy (0.789), with a high R2 value (0.51). Variable importance in projection scores showed thatM. racemosusabundance had the same impact in the model as waist-to-hip ratio, high-density lipoprotein-cholesterol, fasting triglycerides or fasting glucose, suggesting thatM. racemosusrelative abundance in the gut may be a relevant biomarker for cardiovascular risk.