The gene mutation occurring with transformation in lymphoplasmacytic lymphoma (LPL) /Waldenström macroglobulinemia (WM) has not been fully elucidated. Herein, we report a 61-year-old man with LPL/WM. In this case, the MYD88 gene mutation appeared with transformation to diffuse large B-cell lymphoma (DLBCL). Bone marrow biopsy revealed the involvement of CD20 positive small plasmacytoid lymphocytes, indicating LPL/WM. However, the samples taken from both the cervical lymph node and the pleural effusion provided a pathological diagnosis of DLBCL. All samples showed the same patterns of surface antigen expressions and immunoglobulin gene rearrangements. Therefore, these lymphomas had identical clonality and were regarded as transformation from LPL/WM to DLBCL. The MYD88L265P mutation has recently been identified in most LPL/WM cases. The gene analysis in this case demonstrated that the MYD88L265P mutation was detectable in only the pleural effusion sample (DLBCL cells), not in the lymphoma cells of the bone marrow (LPL/WM cells). Thus, it was concluded that LPL/WM had transformed into DLBCL with the MYD88L265P mutation in this patient.