Echinococcosis is a disease resulting from infection by flatworms of the Echinococcus genus. The vast majority of cystic echinococcosis cases in Southern Brazil are caused by Echinococcus granulosus and Echinococcus ortleppi. Here, we surveyed the protein contents of the hydatid fluid compartment of E. granulosus and E. ortleppi pulmonary bovine cysts, in an attempt to compare their molecular arsenal in this host-parasite interface. We detected some molecular players equally in E. granulosus and E. ortleppi, such as proteolytic enzymes and development signaling molecules, while some activities were more evident in one species, such as apoptosis in E. ortleppi, and cysteine protease activity in E. granulosus.