Microfocus X-ray computed tomography (micro-CT) is expected to be utilized in the taxonomy of macroturbellarians that require histological technique(s) for identification, allowing nondestructive observation of the internal structures of specimens in a short time. With micro-CT, we observed a polyclad flatworm, Paraplanocera oligoglena (Schmarda, 1859), in this study. In the CT images, the main reproductive organs in the polyclad specimen were well observed, but some diagnostic characters were unclear or undetectable. We also prepared histological sections from the CT-scanned specimen. The histological sections were still observable and we could confirm the structures that were indistinct in the CT images; however, dye-affinity of tissues was slightly altered compared with those in usual sections. Integrating information from micro-CT images and subsequent histological observations, we successfully generated a 3D model of the reproductive organs of the polyclad. Our results suggest that the micro-CT imaging, as of the current resolution, would not completely replace the traditional histological technique; instead, these two techniques need to complement each other for a better understanding of the morphology that underpins the polyclad systematics.