Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA), which often produces Panton-Valentine leucocidin (PVL), has emerged worldwide as a life-threatening pathogen. Herein, we describe molecular characteristics of MRSA isolated from abdominal cellulitis in a 7-year-old Japanese boy. This MRSA was PVL-positive and belonged to the Taiwanese multiple drug-resistant CA-MRSA clone with the genotype of ST59, staphylococcal cassette chromosome mec (SCCmec) VII (SCCmecV, according to recent reclassification), agr1a (a novel agr1 subtype), and SaPI (which carried seb1, a newly designated variant seb gene). This study demonstrates the first isolation of the Taiwanese PVL-positive ST59 MRSA clone in Japan. The data also demonstrate novel subtypes in agr1 and seb and suggest that a combination of agr1a, seb1, and PVL could contribute to cellulitis (and its recurrence). Recently, a variety of PVL-positive MRSA clones are accumulating in Japan.