Flounder, Paralichthys orbignyanus (Valenciennes), were captured in polluted and non-polluted sites within the Patos Lagoon Estuary, southern Brazil, over four seasons. Blood films showed a high prevalence of infection with a haemogregarine, or mixed parasitaemias of this and an organism resembling Haemohormidium terraenovae So, 1972. Haemogregarine gamont stages conformed to existing descriptions of Desseria platessae (Lebailly, 1904) Siddall, 1995 from flatfishes, but intraerythrocytic division of meronts was observed, leading to the recommendation for nomenclatural correction, placing the haemogregarine in the genus Haemogregarina (sensu lato) Danilewsky, 1885. Statistical analyses suggested that although sample sizes were small, infections with meront stages, immature and mature gamonts were all influenced by site, and possibly therefore, by pollution. Season also appeared to determine likelihood of infection with meronts and immature gamonts, but not mature gamonts, while adult fish gender apparently affected infection with immature and mature gamonts, but not meronts. The H. terraenovae-like organism exhibited unusual extracellular forms and did not match closely with the type description of H. terraenovae; precise identification was therefore difficult. Data analyses suggested that parasitism by this organism was influenced by site and fish gender, since females and males from non-polluted water were infected, but only females from the polluted site. Season was also important and significantly more adult fish of both sexes were infected with this parasite in the Brazilian summer and autumn, compared with winter and spring. Finally, these appeared to be the first observations of Haemogregarina platessae, and possibly H. terraenovae, from the southern hemisphere.