Between March 2003 and February 2007, the livers and the lungs of 2,231 horses from various Italian regions were examined for cystic echinococcosis presence at the time of slaughter. Hydatid cysts were found in six horses, namely four from Sardinia, one from Sicily, and one from Tuscany. The location, number, morphology, and fertility of the cysts found were determined. DNA was extracted from the germinal layers and protoscoleces of the fertile cysts and polymerase chain reactions (PCR) were performed in order to strain type DNA isolates for reduced nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1), cytochrome c oxidase subunit 1 (CO1) and 12S partial genes. The PCR products were then purified and sequenced in forward and reverse. Hydatid materials obtained from positive animals were identified as Echinococcus granulosus s.s. (old G1, sheep strain) and Echinococcus equinus (old G4, horse strain) for ND1, CO1, and 12S partial genes. This allowed us to record the presence of the E. equinus in Italy for the first time with molecular tools and also to report new data on the epidemiological situation of this parasite in Italy.