Melissococcus plutonius infects honeybee larvae and causes European foulbrood (EFB). Because of its highly contagious and difficulties seen in eradication, this disease is only selected as the OIE-listed notifiable bacterial honeybee diseases together with American foulbrood (AFB). According to studies on comparison of proteins or DNA fragment profiles M. plutonius has been believed to be remarkably genetically homologous. However, M. plutonius-like organisms with several different characteristics but shown typical clinical signs of EFB have often been isolated from diseased larvae in Japan. To understand this pathogen, we have done the complete genome sequencing of various M. plutonius isolates.