Hepatic infection involving a parasite of the family Calyptosporidae was recorded in characiform fish from the Tocantins river in the Brazilian Amazon region. In the present study, an integrated comparative analysis of morphological characteristics, histological and structural traits, and the sequence of a partial fragment of the SSUrRNA gene provides support for the identification of a new calyptosporid species, found parasitising the hepatic tissue of the fish Triportheus angulatus, collected from the Tocantins River. This new species was named Calyptospora gonzaguensis n. sp. and had ovoid oocysts with a diameter of 19.6 AE 1.4 lm and four peripheral sporocysts, 9.2 AE 0.6 lm long and 3.9 AE 0.2 lm wide, enveloped individually in fine adhesive membrane, composed of an ellipsoid body and posterior extension, with a mean length of 2.2 AE 0.4 lm.