Odontogenic myxofibromas are variants of odontogenic myxomas that contain considerable amounts of collagen fibers in the myxoid stroma. Cytogenetic studies of odontogenic myxomas/myxofibromas have rarely been reported. This report describes the first case of an odontogenic myxofibroma presenting with HMGA2 protein overexpression and HMGA2 rearrangement in a 40-year-old woman. A 2.7-cm tumor in the premolar region of the right mandible was curettaged. There was no evidence of recurrence or metastasis at 12 months after the surgery. Histological examination revealed that the tumor comprised spindle or stellate cells with mild nuclear pleomorphism, abundant myxoid matrix and partly dense collagen fibers. Mitotic figures were rarely observed. Immunohistochemically, the tumor cells were diffusely positive for vimentin and HMGA2. Less than 1% of the tumor cells were positive for Ki-67. We detected split signals by interphase fluorescence in situ hybridization (FISH) in paraffin sections using HMGA2 break-apart probes. The breaks were certainly located within or near the HMGA2 gene. No rearrangement of the FUS gene was detected by FISH, implying discrimination from low-grade fibromyxoid sarcoma. It is suggested that HMGA2 rearrangement and HMGA2 protein overexpression may be associated with the tumorigenesis of odontogenic myxomas/myxofibromas, similar to the case for many other benign mesenchymal tumors.