The obligate root parasite Cistanche armena is a recently rediscovered, extremely rare endangered species endemic to Armenia, specifically parasitizing camelthorn (Alhagi maurorum, Fabaceae) and saltwort (Salsola dendroides, Chenopodiaceae). Its populations are reputedly declining due to habitat destruction and biotic impacts. Since the only known means of its reproduction is via the seeds, understanding the mechanisms of breaking C. armena seed dormancy and germination along with the related aspects of the species’ biology is highly important both from fundamental (functional ecology and evolution) and applied (conservation and management) perspectives. Here, we present the first in vitro seed germination protocol for C. armena involving fluridone, a systemic herbicide targeting the carotenoid biosynthetic pathway. In addition, the seed micromorphology of C. armena is described using both light microscopy and lignin autofluorescence visualized by confocal laser scanning microscopy. The actin cytoskeleton in radicle cells of germinated C. armena seedlings is described for the first time, being the proof of seed viability. Further elaboration and application of the proposed germination protocol with the cultivation of C. armena on susceptible hosts are altogether seen as a valuable tool for the conservation of this species.