Two major type of lymphoma involve the pleura as primary neoplasms: primary effusion lymphoma (PEL) in the setting of human immunodeficiency virus (HIV) infection, and pyothorax-associated lymphomas (PAL), with a strong Epstein-Barr virus (EBV) or pyothorax association. However, indolent B cell lymphoma initially manifested as pleural effusion is an extremely rare clinical occurrence. In this study, we report a case of 52-year-old woman with no history of HIV infection or pyothorax, who only manifested long-term massive bilateral pleural effusion. This patient was characterized by lymphocytic pleural effusion, which had been misdiagnosed as tuberculous hydrothorax. A total of 75 liters of pleural effusion were drained over a two-year period. After admission to our hospital, we performed flow cytometry of pleural effusion and revealed proliferation of B lymphocytes with abnormal immune markers consistent with marginal zone B cell phenotype, although lymphocyte morphology is normal. Flow cytometry on bone marrow revealed ckappa restrictive expression on B cells further, which indicating small B cell lymphoma. The right-side pleural fluid was encapsulated after thoracoscopy and the patient's symptom were relieved. Considering the foreseeable side effects of chemotherapeutic drugs and indolent potential of the small B cell lymphoma, the patient opted not to undergo further treatment. Follow up was done 1, 3 and 6 months after discharge, the depths of bilateral pleural effusion on ultrasound stabilized around 3 cm without thoracentesis. This case is thought to be an unusual presentation because the pleural lymphoma occurred on an immunocompetent adult woman and the type was small B cell lymphoma, which were totally different from PEL or PAL. We also describe the use of flow cytometry to effectively diagnose the unexplained pleural effusion, and discuss the findings using relevant previously reported literature. Overall, our findings provide new insights to deal with unexplained pleural effusion and the value of flow cytometry in diagnosis.