Echinococcus multilocularis metacestodes possess an alkaline phosphatase (EmAP) which has been extensively characterized at the biochemical level in previous studies. The apparent molecular weight of the enzyme monomer and its isoelectric point matched those originally described for the Em2 antigen, a reference antigen currently used for the immunodiagnosis of E. multilocularis infection. These observations raised questions about the molecular relationship between the two molecules. In order to investigate the relations between EmAP and the Em2 antigen, immunoblotting and ELISA were carried out using polyclonal and monoclonal antibodies directed against EmAP and the Em2 antigen, respectively. In addition, the localization of EmAP and the Em2 antigen was compared by immunofluorescence and immunogold electron microscopy in in vitro-generated E. multilocularis metacestodes. The results show that common epitopes between EmAP and Em2 exist, which are predominantly of a peptidic nature. Both antigens are localized in an acellular parasite structure, the laminated layer, with additional locations for the EmAP on the glycocalyx and in the central region of invaginated protoscoleces. These results suggest a putative functional relationship between the two antigens and that Em2 could originate from EmAP.