This report describes a case of extranodal marginal zone B-cell lymphoma (ENMZL) of the mucosa-associated lymphoid tissue (MALT) lymphoma that transformed to diffuse large B cell lymphoma (DLBCL) in a 39-year-old female patient with Hashimoto's thyroiditis (HT). The patient presented with MALT lymphoma in the thyroid tissue and DLBCL in the multiple site invasions, including the ovary, breast, and lymph nodes. We assessed the Ig gene rearrangement and mutation profile in lymphoma involved tissues and the collected stem cells. V(D)J sequence of the tumor clonotype detected in thyroid, ovary, and breast was identical, revealing a shared origin of the malignant lymphoma. Noticeably, a small percentage of tumor clonotype (the highest-ranking clonotype in tumor tissues) was detected in the stem cell sample, suggesting the malignant cells was residual in the stem cells, likely conferred disease relapse following ASCT. This patient recieved BTK inhibitor combined with radiotherapy to eradicate the residual tumor cells based on the V(D)J sequence monitoring after ASCT. Now the patient remains in complete remission following 12 months of ASCT.Copyright © 2023. Published by Elsevier GmbH.