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Abstract: The mangrove oyster, Crassostrea rhizophorae (Bivalvia, Ostreidae) is commonly collected by fisherwomen in the estuaries of the Ceará State (CE), Northeastern Brazil. Despite the socioeconomic importance of this natural resource, there are few studies on the health of the oysters in this region. This study aimed to survey pathological changes in the mangrove oyster C. rhizophorae in the estuary of the Pacoti River, CE. Adult oysters were collected in August 2008 (N =450) and December 2009 (N =450) at three sites of the Pacoti estuary and in 2010 (N =600) samplings were done quarterly at one site which has showed the higher prevalence de Perkinsus. Macroscopical and histological analyses were used to evaluate pathological changes, Ray’s Fluid Thioglycollate Medium (RFTM) to detect Perkinsus spp. and polymerase chain reactions (PCR) and DNA sequencing to identify Perkinsus species. In 2009, RFTM assay detected Perkinsus sp. infecting the tissues of C. rhizophorae with low prevalences of 1.3%, 6.7% e 7.3% in sites 1, 2 and 3, respectively, and in 2010, in site 3, prevalence was 2% (12 of 600 oysters). PCR did not confirm any positive case in 2009 and only 5 in 2010. The phylogenetic analyses strongly indicate that the Perkinsus species infecting oysters C. rhizophorae of this study belongs to Perkinsus beihaiensis. The histology confirmed 11 cases of Perkinsus sp. infecting the C. rhizophorae in 2009, and only two cases in 2010. Nematopsis sp. was the protozoan observed with greater prevalence (up 96.7%). Other found protozoa were: Trichodina, Sphenophrya, Ancistrocoma – like and an unknown ovarian parasite. The metazoa found were the polychaete Polydora with high prevalences, a turbellarian, possibly of the genus Urastoma, an unidentified digenean metacercariae and larvae of cestode Tylocephalum. A continuous monitoring of diseases in bivalves from this natural population is recommended, since the phylogenetic analyses indicate the occurrence of P. beihaiensis infecting oysters C. rhizophorae whose pathogenic potential is unknown. [Copyright &y& Elsevier]