Staphylococcus lugdunensis is a Gram-positive, coagulase-negative Staphylococcus (CNS) species that is found as a skin commensal and has been implicated in fulminant invasive diseases such as infective endocarditis. S. lugudunensis infections resemble Staphylococcus aureus infections in terms of virulence, tissue destruction and clinical course. Although correct identification and determination of the susceptibility profile are important, some commercial systems may misidentify S. lugdunensis. We report a case of native valve infective endocarditis caused by S. lugdunensis, which was misidentified by the Vitek 2 system but identified correctly by 16S ribosomal RNA (rRNA) gene sequencing in a 72-year-old male patient. The patient had multiple vegetations on his mitral valve, and the largest one was found on the posterior mitral valve leaflet. It was 2.5 cm in size and hypermobile. Diffuse valvular abscess was also observed. He had persistent bacteremia for appoximately 8 days, which was resolved after immediate surgery and antibiotic therapy. When a patient with severe sepsis syndrome grows S. aureus or CNS other than S. lugdunensis on a commercial automatic culture system, the possibility of S. lugdunensis should be considered and further confirmatory testing such as 16S rRNA sequencing may be very useful.