Myxosporean genera Henneguya and Myxobolus (Bivalvulida: Myxobolidae) are closely related in morphology and molecular phylogeny, speciose with approximately 1,000 nominal species. The majority of them are recorded from freshwater fish worldwide, and few are known from marine fish. In this study, three myxobolid spp. are described from marine fish around Japan. Two novel Henneguya spp., Henneguya ogawai sp. n. and Henneguya yokoyamai sp. n., are described from two black sea breams (Acanthopagrus schlegelii) fished in the Inland Sea (Setonaikai), Japan. Plasmodia of the former species were localized in the esophageal or intestinal wall, and those of the latter species were in the wall of the gall bladder and peritoneum. Spore development in plasmodia of these two species was synchronous. The spore body of H. ogawai sp. n. was 11.0 (8.9-12.2) μm in length, 6.9 (6.3-7.5) μm in width, 5.9 (5.2-6.6) μm in thickness, with a bifurcated caudal process of equal length, 10.0 (8.4-12.7) μm long; total spore length, 21.1 (19.2-23.4) μm. It contained two polar capsule, 4.3 (3.8-5.2) × 1.9 (1.4-2.3) μm. The spore body of H. yokoyamai sp. n. was 11.0 (10.1-13.7) μm in length, 7.1 (6.6-7.5) μm in width, and 5.6 (4.5-6.4) μm in thickness, with a bifurcated caudal process of equal length, 14.1 (10.8-17.0) μm long; total spore length, 25.0 (21.9-29.2) μm. It contained two polar capsules, 3.7 (3.1-4.2) × 2.0 (1.8-2.4) μm. A novel Myxobolus sp., Myxobolus machidai sp. n., is described from a spotted knifejaw (Oplegnathus punctatus) fished in the Sea of Japan, off Shimonoseki, Yamaguchi Prefecture, Japan. Plasmodia were embedded in the esophageal wall. Its round spore was small in size, 9.0 (8.1-9.4) μm in length, 7.8 (7.5-8.3) μm in width, and 5.5 (5.1-6.0) μm in thickness. It contained two polar capsules, 3.5 (3.2-3.8) × 2.3 (2.2-2.5) μm. Spore development in a plasmodium was asynchronous. Nucleotide sequencing of the small subunit ribosomal RNA gene (SSU rDNA) of these two novel Henneguya spp. revealed a close phylogenetic relationship with the marine clade of Henneguya spp.; however, they were distinct in morphology and SSU rDNA sequence from any known species. M. machidai sp. n. was grouped with freshwater Henneguya spp. in a phylogenetic tree based on the SSU rDNA, distant from a known marine clade of Myxobolus spp. reported mainly from the Mediterranean Sea. This is the first record of Henneguya-Myxobolus spp. from natural marine water in Japan.