We present a case of struma ovarii with unique histological features. A 57-year-old woman presented with a 13-cm multilocular cystic ovarian tumor. Histological examination demonstrated both differentiated (follicular patterns) and de-differentiated (diffuse, trabecular and small-sized solid nests) patterns, suggesting a histological diagnosis of struma ovarii. To identify the pathogenesis of the tumor, immunohistochemical (TTF1, thyroglobulin, T3, E-cadherin, ZEB1, Slug, and Twist) and genetic (KRAS and BRAF) analyses were performed. TTF1, thyroglobulin, and T3 were detected in both tumor components. Additionally, although E-cadherin was detected in the differentiated component, loss of E-cadherin was obvious in the de-differentiated component. Finally, we examined ZEB1, Slug, and Twist expression to identify the role of epithelial-mesenchymal transition (EMT) in tumor pathogenesis. Slug, ZEB1, and Twist were not expressed in the differentiated component, but ZEB1 expression was observed in the de-differentiated component. Moreover, no KRAS or BRAF mutations were detected in either component. These findings suggested that the histological transition from the differentiated to de-differentiated tissue was closely associated with the loss of E-cadherin expression. This loss may have been related to increased ZEB1 expression and lack of neoplastic features due to the absence of KRAS and BRAF mutations.