The occurrence of anti-Toxoplasma gondii and Neospora caninum in dogs from the municipality of Natal, RN, Brazil, was determined. Information about the presence of these coccidia in this species was not known. Blood samples were collected from 29 domiciled dogs which inhabit areas that surround two important protected areas of Atlantic Forest (Parque da Cidade and Parque das Dunas) and another 73 dogs that were sacrificed due to Leishmania spp. infection, in Center for Control of Zoonosis (CCZ) for the municipality of Natal. It was only possible to obtain information about the gender of dogs that live in the parks area. The presence of antibodies against each parasite was determined by indirect Fluorescence Antibody Test (IFAT), with a cutoff of 16 for T. gondii and 50 for N. caninum. Of the 102 dogs examined, 13 (12.7%, 95% CI 7.0-20.8%) were T. gondii positive and three (2.9%, CI 0.6-8.4%) for N. caninum. Association between: localities of obtaining samples (parks x CCZ) and sex of animals, with the occurrence of antibodies against each of the parasites, was determined by the Fisher exact test. For T. gondii association was found with males (p = 0.027) and dogs living close to parks (p = 0.008) had higher rates of infection. Associations were not observed in relation to N. caninum.