A new species of Microsporidia Microgemma carolinus n. sp. found in the marine teleost Trachinotus carolinus collected in Florianópolis, Brazil was described based on light, ultrastructural and phylogenetic studies. This parasite developed in the liver forming whitish xenomas that contained different developmental stages with monokaryotic nuclei. The periphery of the xenoma presented some vacuolization and possessed several small projections in the membrane. The mature spores, measuring 3·8 ± 0·4 μm in length and 2·4 ± 0·4 μm in width, were slightly pyriform to ellipsoidal and had rounded ends. The polaroplast was bipartite and the isofilar polar filament was coiled with 8 – 9 turns in a single or double row at the posterior end of the spore. The nucleus was voluminous and in a central position, measuring ∼0·9 μm in diameter. A large posterior vacuole appeared as a pale area, occupying about a third of the spore length. The SSU rRNA gene was sequenced and analysed using maximum parsimony, maximum likelihood and neighbour-joining methods. This study allowed us to conclude that this was a new species of the genus Microgemma, being the first description of this genus from among South America fauna.