Two myxozoan species were observed in the kidney of topsmelt, Atherinops affinis, during a survey of parasites of estuarine fishes in the Carpinteria Salt Marsh Reserve, California. Fish collected on 3 dates in 2012 and 2013 were sectioned and examined histologically. Large extrasporogonic stages occurred in the renal interstitium of several fish from the first 2 collections (5/8, 11/20, respectively) and, in some fish, these replaced over 80% of the kidney. In addition, presporogonic and polysporogonic stages occurred in the lumen of the renal tubules, collecting ducts, and mesonephric ducts. The latter contained subspherical spores with up to 4 polar capsules, consistent with the genus Chloromyxum. For the third collection (15 May 2013, n = 30), we portioned kidneys for examination by histology, wet mount, and DNA extraction for small subunit ribosomal (SSU rDNA) gene sequencing. Histology showed the large extrasporogonic forms in the kidney interstitium of 3 fish and showed 2 other fish with subspherical myxospores in the lumen of the renal tubules with smooth valves and 2 spherical polar capsules consistent with the genus Sphaerospora. Chloromyxum-type myxospores were observed in the renal tubules of 1 fish by wet mount. Sequencing of the kidney tissue from this fish yielded a partial SSU rDNA sequence of 1,769 base pairs (bp). Phylogenetic reconstruction suggested this organism to be a novel species of Chloromyxum, most similar to Chloromyxum careni (84% similarity). In addition, subspherical myxospores with smooth valves and 2 spherical polar capsules consistent with the genus Sphaerospora were observed in wet mounts of 2 fish. Sequencing of the kidney tissue from 1 fish yielded a partial SSU rDNA sequence of 1,937 bp. Phylogenetic reconstruction suggests this organism to be a novel species of Sphaerospora most closely related to Sphaerospora epinepheli (93%). We conclude that these organisms represent novel species of the genera Chloromyxum and Sphaerospora based on host, location, and SSU rDNA sequence. We further conclude that the formation of large, histozoic extrasporogonic stages in the renal interstitium represents developmental stages of Chloromyxum species for the following reasons: (1) Large extrasporogonic stages were only observed in fish with Chloromyxum-type spores developing within the renal tubules, (2) a DNA sequence consistent with the Chloromyxum sp. was only detected in fish with the large extrasporogonic stages, and (3) several Sphaerospora species have extrasporogonic forms, but they are considerably smaller and are composed of far fewer cells.