Rearing cattle and goats is an important economic activity for smallholder farmers in Mozambique where animals are raised in traditional production systems in communal pastures. Despite its importance, there is little information on their health conditions, particularly the occurrence of infections by parasites that can cause economic losses, especially Neospora caninum and Besnoitia besnoiti. A serological study to estimate the prevalence of Neospora caninum and Besnoitia besnoiti was undertaken in Angónia district of Central Western Mozambique between April and May 2010. Animals were randomly selected at acaricide dip tanks upon the consent of the owners, and all the selected animals were regarded as one flock in each locality. A serological survey for these protozoa was undertaken using the Indirect Fluorescent Antibody Test. A prevalence of anti-N. caninum IgG was estimated in 297 cattle serum samples and 8.4% were positive at the dilution of 1:200 to 1:800, while in goats from the 132 samples 3.8% were positive at 1:50 and 1:100 dilutions. Ninety four cattle samples were examined and 39.4% were positive for anti-B. besnoiti antibodies, which represents a high prevalence. This is the first evidence of seroprevalence of N. caninum in cattle and goats, and of B. besnoiti in cattle in Angónia, Mozambique.