The development and integration of DNA-based methods in research and clinical microbiology laboratories have enabled standardised and comprehensive detection and differentiation of the microbes colonising our guts. For instance, the single-celled parasites Blastocystis and Dientamoeba appear to be much more common than previously thought, especially so in healthy individuals. While increasing evidence appears to suggest limited pathogenicity of these parasites, next-generation-sequencing-based studies have helped us to appreciate links between parasite colonisation and certain host phenotypical characteristics and gut microbial profiles. The fundamental question remains as to whether such parasites are merely indicators or active manipulators of gut microbiota structure and function. In this article, we collate existing evidence that these parasites are, at minimum, indicators of intestinal microbiota structure. The development and implementation of DNA-based technologies in microbiology laboratories have helped us to understand that single-celled parasites such as Blastocystis and Dientamoeba are far more common than previously anticipated. Colonisation by these parasites appears to be negatively associated with symptoms of severe gastrointestinal disease and high body mass index. Hence, these parasites are most common in individuals with a healthy gut, while less prevalent in patients with irritable bowel syndrome, and even less common in patients with inflammatory bowel disease. Moreover, Blastocystis is more common among normal-weight individuals than among overweight and obese individuals. Several recent studies suggest that certain microbial communities are linked to the presence of parasites such as Blastocystis and Entamoeba. Indeed, the gut microbiota of a given person can, to some extent, be predicted by parasite colonization status – and vice versa. We hypothesise that colonization by parasites such as Blastocystis is dependent on gut physiological conditions such as hypoxia, and that colonization is seen only in individuals with eubiosis rather than dysbiosis, that is, a predominance of anaerobic bacteria of high diversity rather than facultative anaerobic bacteria such as, for example, Enterobacteriaceae.