Background: Schistosomiasis is neglected tropical parasitic disease affecting both humans and animals. Due to the human health impact, population genetic studies have focused on the three main human-infecting schistosome species: Schistosoma mansoni, S. haematobium and S. japonicum. Here we present novel data on the population genetic structure of Schistosoma bovis, a highly widespread and prevalent schistosome infecting ruminants, and therefore of veterinary importance. Methods: Adult S. bovis were sampled in the two main abattoirs of Cameroon (Yaoundé and Douala). Twenty-two cows originating from four distinct localities were sampled and a total of 218 parasites were recovered. All parasites were genotyped using a panel of 14 microsatellite markers and a sub-sample of 91 parasites were sequenced and characterized with the mitochondrial (cox1) and nuclear (ITS) genetic markers. Results: No significant difference in allelic richness, heterozygosity, nucleotide diversity and haplotype diversity was observed between the populations. Additionally, no strong genetic structure was observed at the country scale. Our data also show that S. bovis is more polymorphic than its sister species, S. haematobium, and that the haplotype diversity is similar to that of S. mansoni while the nucleotide diversity does not significantly differ from that of S. haematobium. The resulting negative Tajima's D* and Fu and Li's D* indices could be a signature of population demographic expansion. No S. haematobium/S. bovis hybrids were observed in our populations, thus all samples were considered as pure S. bovis. Conclusions: This study provides novel insights into genetic diversity and population genetic structure of S. bovis. No strong genetic structure was observed at the country scale but some genetic indices could be associated as a signature of population demographic expansion.