Several studies show the presence of protozoa of the genus Nematopsis Schneider, 1892, in many species of bivalves. The pathogenicity of this Apicomplexa is still much debated, which is possibly related to the parasitism degree and host habitat. In this context, this study investigated parasitism by Nematopsis sp. in Mytella guyanensis (Bivalvia: Mytilidae) in a mangrove of the Marine Extractive Reserve Baía do Iguape, Bahia, Brazil. The collections were made monthly, from March 2014 to March 2015, consisting of 30 adults with shell height above 40 mm per month, totaling 360 specimens. The specimens were measured, weighed, opened, and macroscopically examined for identifying parasites and/or signs of morphological changes. After that, they were fixed in Davidson’s solution and processed according to classical histological techniques, with inclusion in paraffin, obtaining 5 μm-thick sections by microtomy, and stained by Harris’ Hematoxylin and Eosin (HE). The water temperature ranged from 25.5 to 33.6 ºC and the salinity from 21.1 to 34.3 Practical Salinity Units (PSU). The specimens measured between 41.1 and 68.6 mm and had an average weight of 7.24 g. Macroscopically, there was no presence of the parasite or any morphological changes related its presence. The frequency percentage of Nematopsis sp. was 99.45%. The mantle was the organ with the highest frequency of infection (46.26%), followed by the gonads (18.36%). Among the analyzed organs, all presented the parasite and, in a few severely infected cases, microscopical changes were observed in the mantle conformation. The infection intensity for most of the sessions analyzed was 1 to 3 oocysts/phagocyte; however, in one of the sessions, 9 oocysts/phagocytes were recorded. The parasite had a negative correlation with salinity. The high frequency of Nematopsis sp. should be considered for the sustainability of natural stocks, especially if such parasitism occurs simultaneously with other pathogens and stressful environmental conditions.