Alveolar (AE) and cystic echinococcosis (CE) are two of the most dangerous helminthic zoonoses worldwide, representing chronic hepatic diseases, often with lethal outcome. Since early diagnosis of echinococcosis is essential for effective treatment, an overview of serological methods for the detection of echinococcosis and differentiation between AE and CE is given. Recombinant antigens Em18 and Antigen B8/1 are highly recommended for patient screening and identification of AE and CE, respectively, in combination with imaging techniques. Novel aspects of molecular phylogenetic studies on the genus Echinococcus will also be addressed, including the description of Echinococcus shiquicus as a new sister-species of Echinococcus multilocularis. Both the serological detection of the disease and molecular phylogeny will be discussed in perspective.