An epidemiological survey of cystic echinococcosis (CE) in cattle and sheep was conducted from October 2009 to October 2011 in endemic areas of north-eastern and southern Romania. A total of 8569 animals (3043 cattle and 5526 sheep) were examined, and hydatid cysts were found in 984 (32.34%) cattle and 2756 (49.87%) sheep, respectively. The average number of cysts per animal was 11.3 (range, 1-47) in cattle and 4.2 (range, 1-16) in sheep. Of the CE-positive animals, 177 (17.9%) of the cattle and 358 (12.98%) of the sheep had hydatid cysts only in the lungs, 62 (6.3%) and 803 (29.13%) had only in the liver, and 723 (73.47%) and 1572 (57.04%), respectively, had hydatid cysts both in the liver and in the lungs. Very few animals had cysts in spleen (19 cattle and 23 sheep) and kidney (three cattle). From a sample of 422 cysts undergoing closer examination (258 from cattle, 164 from sheep), the highest fertility rate (38.41%) was found in sheep cysts, while from the cattle only four cysts (1.55%) were found to be fertile. Species identification of 13 animal isolates (nine from sheep, four from cattle) and one human isolate were done by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the mitochondrial nad1 gene and confirmed by partial sequencing of the cox1 gene. All showed the same RFLP band pattern (Echinococcus granulosus sensu stricto) and were identified as the "sheep strain" G1 by sequencing. The study emphasizes the hyperendemic presence of E. granulosus in Romania and outlines the necessity for the urgent development of sustainable surveillance and control strategies both in animals and humans.