We present a case of primary malignant lymphoma of the prostate in a 77-year-old Japanese man. Immunohistochemical examinations revealed the presence of a non-GCB subtype of DLBCL (CD10 (-), Bcl-6 (-), MUM1 (+)), and genetic analysis disclosed a lack of typical codon 206 or 265 missense mutation in MYD88, suggesting that the case was of type3 (non-GCB andnon-ABC), a subtype of DLBCL. Three courses of chemotherapy (rituximab in combination with cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP)) were effective, and the patient has been free of the disease with no local or systemic recurrence for three years. Although the significance of silent mutation at hot spot of the highly oncogenic MYD88 gene in this case is unclear, a minute increase in translational efficiency by silent mutation may have contributed to the activation of MYD88.