A new species Ellipsomyxa syngnathi sp. n. (Myxozoa) is described from Syngnathus typhle L. and Syngnathus rostellatus Nilsson, 1855 (Syngnathidae), using spore morphology and SSU rDNA sequence data. Monosporic plasmodia develop in the internal gallbladder wall. The ellipsoid myxospore has two pyriform polar capsules which discharge at opposite sides some distance from both sutural line and spore ends. The myxospore mainly differs from that of Ellipsomyxa gobii Køie (Folia Parasitol 50:269-271, 2003) in being monosporic and in having the sutural line oblique to the thickness axis. Zschokkella mugilis Sitjá-Bobadilla and Alvarez-Pellitero (J Euk Microbiol 40:755-764, 1993) is transferred to Ellipsomyxa as Ellipsomyxa mugilis comb. n.