In order to estimate the seroprevalence and to assess risk factors of Toxoplasma gondii and Neospora caninum in the province of Nyanga, in southern Gabon, a cross-sectional study was conducted in sheep and goats in the county of Mongo. Serological screening was performed using an indirect multi-species enzyme-linked immunosorbent assay and a commercial direct agglutination test to test serum samples for the presence of anti-N. caninum and anti-T. gondii Immunoglobulines (Ig) G antibodies, respectively. From a total of 201 small ruminants, including 95 sheep and 106 goats, the overall anti-N. caninum and anti-T. gondii IgG seroprevalences were 31.3% (n=63) and 45.8% (n=95), respectively. Statistical analyses showed that adult small ruminants were 4 times more likely to be infected with T. gondii than young animals (p<0.001; OR=4.27; 95% CI: 2.07-8.81). The locality was significantly associated with T. gondii seropositivity (p=0.001). The Dilemba (p<0.001; OR=0.07), Moulengui-Binza (p=0.023; OR=0.05) and Rina-Nzala localities (p=0.005; OR=0.1) were not identified as risk localities associated with T. gondii infection. The seroprevalence of N. caninum was significantly higher in sheep (42.1%) than goats (21.7%). The species was not associated with N. caninum infection (p=0.005; OR=0.27; 95% CI: 0.11-0.68). In Bibora, small ruminants were almost 4 times more likely to get Neospora infection than the animals in the other localities (p=0.04; OR=3.98; 95% CI: 1.06-14.93). The serological prevalence of N. caninum and T. gondii could suggest a considerable impact on the reproductive process from these pathogens in sheep and goats within the Mongo County and a high exposure of humans to T. gondii.