We report a case of primary marginal zone lymphoma in the thymus of a 34-year-old woman. She was initially suspected of having a mediastinal plasmacytoma because of the presence of dominantly proliferating plasmacytic cells in a small fragment obtained by thoracoscopic biopsy, and an elevated level of serum monoclonal IgA. However, histology of the tissue obtained by a subsequent open surgical biopsy revealed diffuse proliferation of atypical monocytoid B-lymphocyte-like cells, which showed prominent plasmacytic differentiation and a close association with thymic epithelial cells consistent with the histology of a marginal zone lymphoma of the thymus. These lymphoma cells were positive for CD19, CD20, IgA, and kappa, and negative for CD5, CD10, and other T/NK-cell and myelomonocyte antigens. Both G-banded and spectral karyotyping analyses revealed the lymphoma cells carried a chromosomal anomaly, 46,X,dup(X)(p11p22). Although large cell type B-cell lymphoma in the thymus (mediastinal diffuse large B-cell lymphoma), which is categorized as a definite subtype in revised European-American classification of lymphoid neoplasms and the new World Health Organization classification, is not infrequent, primary marginal zone lymphoma of the thymus is extremely rare. To our knowledge, this is the first case report of primary marginal zone lymphoma of the thymus with a detailed chromosomal analysis.