Three species of penaeid shrimp, Fenneropenaeus indicus, Penaeus monodon and P. semisulcatus, found in trawler catches off the west coast of Madagascar were infected with microsporidian parasites. The infections were evident as muscular lesions with a cottony appearance when abundant. Spore size (2.6 x 1.6 microm) and morphology (ovoid) for the parasites infecting both F. indicus and P. semisulcatus were not significantly different, suggesting that they might be the same microsporidian species. Spore size (1.4 x 1.1 microm) and morphology (sub-globose to ovoid) in P. monodon infections were significantly different from those in the other 2 shrimp species, suggesting that it was a different parasite. The presence of microsporidians in this biogeographical zone means that there is a potential risk of infections of cultured shrimp in farms situated in the vicinity. This must be assessed by increasing current knowledge of the parasites.