A 5-yr-old, captive, hatched, female false gharial (Tomistoma schlegelii) presented with a 1-mo history of cervical spinal curvature. Antemortem diagnostics, including blood work, electromyography, muscle biopsies, and advanced imaging tests, were either within reference ranges or did not identify any specific etiology. Necropsy revealed extensive, marked, chronic granulomatous encephalomyelitis along with neuronal necrosis, rarefaction, gliosis, and astrocytosis of the white and gray matter of the cerebrum, cerebellum, brainstem, and spinal cord. Pan-chlamydiae polymerase chain reaction protocols for the 16S ribosomal RNA and ompA genes were performed on samples of spinal cord and brain, and both resulted in amplicons. Sequencing of the products revealed that they were positive for a novel Chlamydia species. Infections by members of the phylum Chlamydiae have been reported in a diverse range of vertebrate hosts, including crocodilians. Chlamydia spp. infections are likely underdiagnosed because of a paucity of diagnostic techniques specific for detection. This is the first case report of a novel Chlamydia species associated with severe granulomatous encephalomyelitis in a false gharial.