We examined 71 faecal samples of carnivores from Queen Elizabeth National Park (QENP), Uganda, for eggs of Echinococcus species. Thirty-nine faecal samples contained taeniid eggs. For species diagnosis, DNA was isolated from a total of 1984 individual taeniid eggs. To differentiate eggs of Echinococcus felidis from other taeniid taxa (including the closely related Echinococcus granulosus sensu stricto), a restriction fragment length polymorphism (RFLP)-PCR of the mitochondrial nad1 gene was developed. As the faecal samples were taken from the environment, the host species was determined for all samples, except for one, by RFLP-PCR of the cob gene. Seven hundred and ninety-one of the 1984 eggs yielded a suitable PCR product. E. felidis was present in 34 of 47 samples from lions, none of 18 samples from leopards, and one of five samples from spotted hyenas. No Echinococcus taxon other than E. felidis was found, but three samples from lions contained eggs of Taenia regis. Two hydatid cysts of warthog origin from QENP were available for this study; molecular examination showed that one belonged to E. felidis, the other to E. granulosus (G1 strain). As a comparison of methods demonstrated that molecular diagnostic tools used for previous surveys of Echinococcus isolates in eastern Africa are not suitable to discriminate between E. felidis and E. granulosus sensu stricto, we re-examined 412 hydatid cyst samples of human, sheep, cattle, camel and goat origin from Kenya. Previous results were confirmed, as E. granulosus sensu stricto and Echinococcus canadensis G6/7 strain, but no E. felidis was found among these samples. In conclusion, we provide evidence that E. felidis is a frequent parasite of lions in Uganda, and possibly also occurs in hyenas. Additionally, we show that warthogs interact as intermediate hosts for E. felidis. We did not find evidence that E. felidis is present in eastern Africa outside conservation areas.