The hidden lifestyle of the holoparasitic perennial Lathraea squamaria L. (common toothwort), which parasitizes the roots of deciduous trees in forests and woodlands, has led to significant knowledge gaps about the mechanisms underlying this plant symbiotic interaction. Here we present the first detailed structural examination of the interface between L. squamaria and its host root belowground using non-destructive micro-computed tomography (micro-CT). To clarify the physiology of seed germination in this elusive species, we demonstrated efficient in vitro germination of L. squamaria seeds. The terminology for the gross morphology and micromorphology of L. squamaria has been revised, and clear microscopic evidence for several previously described structures (e.g., prehaustoria, haustoria, seeds, elaiosomes, nectaries, and pollen) has been provided. Generally, this research aims to deepen our understanding of parasitic interactions, phenology, as well as the ecological significance of L. squamaria and its biotic associates (e.g., feeders and pollinators) within forest ecosystems.