Background: Bacteroides dorei is an anaerobic, gram-negative bacterium first described in 2006. Due to the high similarity in mass spectrum patterns between B. dorei and Bacteroides vulgatus, discriminating these species is arduous in clinical practice. In recent decades, 16S rRNA gene sequencing has been a complementary method for distinguishing taxonomically close bacteria to the genus and species levels, including B. dorei and B. vulgatus. Accordingly, B. dorei has been shown to contribute to some diseases, including type 1 autoimmune diabetes mellitus and atherosclerotic diseases. Nevertheless, there are no reports on invasive infectious disease caused by B. dorei. This report describes the first case of B. dorei presenting direct invasion and colonisation into human tissue, providing a warning for the previously proposed application of B. dorei as live biotherapeutics for atherosclerotic diseases.Case presentation: A 78-year-old man admitted with suspicion for mycotic thoracic aortic aneurysm was diagnosed by enhanced computed tomography scan, exhibiting the appearance of infection and dissection at the distal aortic arch. Despite strict blood pressure control and empirical antibiotic therapy, the patient's condition worsened. For the prevention of aneurysmal rupture and elimination of infectious foci, the patient underwent surgical treatment, and the resected specimen was subjected to tissue culture and 16S rRNA gene sequencing analysis to identify pathogenic bacteria. A few days after the surgery, culture and sequencing results revealed that the pathogen was B. dorei/vulgatus and B. dorei, respectively. The patient was successfully treated by appropriate antibacterial therapy, improved and was transferred to another hospital for rehabilitation at postoperative day 34. There was no recurrence of symptoms after the patient transfer.Conclusions: This report describes the first case of invasive infectious disease caused by B. dorei, casting a shadow over its utilisation as a probiotic for atherosclerotic diseases.