This study reports the monitoring of several emerging viral pathogens in Mauritania, which was carried out by the analysis of bovine and camel samples taken at the slaughterhouse of Nouakchott. Blood and serum were collected by random sampling from 159 camels and 118 cattle in March 2013 at the large animals abattoir in Nouakchott. Serological tests for Rift Valley Fever (RVF), Peste des Petits Ruminants (PPR), West Nile disease (WND), epizootic haemorrhagic disease (EHD) and African horse sickness (AHS) were carried out using commercial ELISA kits. The samples, which resulted positives for PPR, WND and AHS, were tested with the confirmatory virus neutralization test (VNT). According to ELISA results, serological prevalence of RVF was 45% (95% CI 52.3–37.7) in camels and 16% (95% CI 22.6–9.4) in cattle. The difference between the observed prevalences in camels and in cattle was significant ( p value ≤ 0.01). PPR was absent in camels and had 12% prevalence (95% CI, 17.86–6.14) in cattle. Furthermore, camels showed 92% (95% CI, 96.1–87.9) prevalence of WNV, 73% (95% CI, 82.3–63.64) of EHD and 3% (95% CI, 5.6–0.4) of AHS. This data are of relevance since provided useful feedbacks on the circulation of the pathogens in field. Moreover, this survey provided new information on the susceptibility of camels to several emerging pathogens and on the possible use of this species as sentinel animal.