Investigations regarding the parasite fauna of wild whitespotted rabbitfish (Siganus canaliculatus) Park, 1797 revealed white, spherical, loosely attached cysts measuring 896 (375–1406) μm in diameter in the inner endothelial wall of the esophagus and stomach. Mature spores inside these cysts corresponded to the original description of spores belonging to the genus Unicapsula Davis, 1924. Unicapsula fatimae n. sp. spores were 6.23 (5.60–6.60) μm in length and 6.80 (6.12–7.39) μm in width. The length of large polar capsule was 2.62 (2.18–2.97) μm and width was 2.65 (2.32–2.90) μm, and the extended large polar capsule filament length was 15.50 (11.71–19.99) μm. Transmission electron microscope images of the plasmodia revealed a complex cyst structure that was unique among other Unicapsula spp. Ultrastructural details of the host–parasite interface and developmental stages of a species from the Unicapsula genus are described for the first time. Histology of an infected esophagus revealed some abnormalities and changes in the host tissue around the infection site, including hypertrophy of host esophagus epithelial cells and hyperplasia of host glandular tubules. The parasite presented here has been added to the genus Unicapsula using comparative morphological analysis and ultrastructural investigations supported by 18S small subunit ribosomal DNA molecular analysis.