The MYD88 L265P somatic variant (MYD88) has a high prevalence in Waldenstrom's Macroglobulinemia (WM), a form of lymphoplasmacytic lymphoma (LPL) associated with monoclonal IgM. Although the role of MYD88 in WM was initially reported in 2012, it was not until 2016 that MYD88 testing was included in the National Cancer Care Network (NCCN) Guidelines. We present a case illustrating the utility of MYD88 status in distinguishing atypical forms of WM from marginal zone lymphoma (MZL) and in selecting second-line therapy with ibrutinib. In 2012, a 64-year-old male presented with dyspnea on exertion, a hemoglobin of 5.6 g/dL, a platelet count of 86,000, and monoclonal IgM kappa on serum immunofixation but no detectable M-spike. Bone marrow biopsy revealed 95% monoclonal B-lymphocytes with lymphoplasmacytic differentiation favoring a diagnosis of LPL/WM over MZL, with a favorable response to chemotherapy. This diagnosis was called into question 3 years later following relapse, and MZL was favored based on the lack of MYD88 mutation. One year later, however, repeat bone marrow biopsy detected the MYD88 mutation and therapy with ibrutinib yielded a favorable response. The distinction between certain lymphomas can be problematic and in this case MYD88 was helpful in clarifying a diagnosis of atypical LPL/WM from MZL and in selecting effective second-line therapy.