Few studies have been carried out in Africa to estimate the prevalence of Taenia hydatigena. With the aim to determine the prevalence of T. hydatigena in slaughtered pigs and small ruminants (goats and sheep) in Mbeya, Tanzania, two cross-sectional surveys were carried out investigating pigs in April to May 2014 and small ruminants in September 2012. In total, 243 pigs were examined post-mortem for T. hydatigena cysts which were found in 16 (6.6 %) pigs. The majority (80 %) of cysts were found on the omentum and the rest on the liver (20 %), all on the visceral surface. Two pigs were also found infected with Taenia solium but showed no signs of other infections. A total of 392 goats and 27 sheep were examined post-mortem, and the prevalence of T. hydatigena was similar in goats and sheep with 45.7 and 51.9 %, respectively. DNA sequencing of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) from a sub sample of metacestodes from goats and sheep confirmed the T. hydatigena infection. The prevalence found in small ruminants was comparable to other studies conducted in Africa, but for pigs, it is one of the highest recorded to date. The present study also confirms the occurrence of T. hydatigena and T. solium in pigs from Mbeya. Further studies are needed to determine the impact of T. hydatigena on production under sub-Saharan conditions and the financial consequences for smallholder farmers.