Abstract The club moss family Lycopodiaceae produces a diverse array of bioactive lycopodium alkaloids (LAs). In particular, the alkaloid huperzine A (hupA) has grasped attention since it is a potent acetylcholinesterase inhibitor of medical interest in Alzheimer's disease. Although the structural diversity and bioactivities of LAs have been studied to some extent, their chemotaxonomic value is mostly unexplored, especially to a lower taxonomic unit (e.g. subspecies or genotypes). This study focused on previously reported Icelandic Huperzia selago genotypes, and aimed to evaluate the chemotaxonomic value of LAs in resolving them. Using liquid chromatography-mass spectrometry (LC-MS), alkaloid fingerprints of H. selago taxa were subjected to principal component analysis (PCA). Our results revealed that each genotype tends to have its own alkaloid profile. Genotype 1 and 3 form distinct groups in a PCA plot, where genotype 2 is an intermediate between the other two genotypes. HupA and its derivative, huperzine B, both contribute to the differentiation of genotype 3 from the others. Therefore, our study demonstrated the potential of alkaloid fingerprints in resolving deep taxonomic groups and selecting plant taxa of medicinal importance.