BACKGROUND: Few studies have focused on eukaryote community in the human gut. Here, the diversity of microeukaryotes in the gut microbiota of an anorexic patient was investigated using molecular and culture approaches. CASE PRESENTATION: A 21-year-old Caucasian woman was admitted in an intensive care unit for severe malnutrition in anorexia nervosa. One stool specimen was collected from the anorexic patient, culture and polymerase chain reaction-based explorations yielded a restricted diversity of fungi but four microeukaryotes Tetratrichomonas sp., Aspergillus ruber Penicillium solitum and Cladosporium bruhnei previously undescribed in the human gut. CONCLUSIONS: Establishing microeukaryote repertoire in gut microbiota contributes to the understanding of its role in human health.