A new species, Myxobolus balantiocheili, is described from the central nervous system of wild and cultured tricolor sharkminnow Balantiocheilos melanopterus from Thailand. The infection was associated with emaciation and severe neurological symptoms, including sudden uncoordinated darting, rolling and pitching. Whitish cysts of varying shape, measuring 70 to 500 µm, were located in the brain, spinal cord and in the meninx, and were sometimes accompanied by haemorrhages. In the brain, most cysts were located in the medulla oblongata and the mesencephalon. Cysts with a segmental distribution were observed in the meninx of the spinal cord. Single di-to hexasporic pansporoblasts, and free mature spores, were frequently seen in both the white and grey matter of the brain and spinal cord, mostly associated with blood vessels. Mature spores varied in shape from oval to ellipsoid, measuring 12.3 ± 0.59 (range 10.6 to 13.3) × 10.0 ± 0.47 (9.2 to 10.9) × 6.9 ± 0.20 (6.7 to 7.1) µm. Spore size and morphology, in addition to fish-host species and apparently narrow tissue tropism, clearly distinguishes this new Myxobolus. No marked inflammatory response or gliosis was associated with the lesions, but compression and degeneration of the nervous tissue surrounding large cysts was observed. We suggest that the high temperature of the fish hosts' tropical habitat may have increased the rate of development and the virulence of M. balantiocheili.