Two new cyclotrypyamine alkaloids equisetinines A and B, as well as three known alkaloids (3–5) were isolated from the stems of Ephedra equisetina Bunge. Their structures were characterized by spectroscopic methods, and the absolute configurations of the new compounds were determined by interpretation of their electronic circular dichroism. Anti-asthmatic activities of compounds were evaluated by releasing β-Hex in C48/80-induced RBL-2H3 cells, and compound 5 exhibited significant anti-asthmatic activities. © 2022 Informa UK Limited, trading as Taylor & Francis Group.