The human gut ecosystem contains an enormous number of microorganisms, including bacteria, archaea, viruses, and fungi. Compared to bacteria, which account for the majority of the gut microbiome, the role of gut fungal species in relation to the host’s metabolic health has received less attention. Nevertheless, with the help of high-throughput sequencing technologies and large-scale human studies, it is now possible to show the influence of gut fungi on several metabolic diseases. In this review, we summarize the current knowledge on the composition of the human gut mycobiome, the methodological developments for characterizing the fungi in the gut, and we provide insights on the possible roles of gut fungi and their underlying mechanisms on metabolic homeostasis and health.