Giardia duodenalis causes over 300 million cases of gastroenteritis (giardiasis) annually, and has unique cell biology shaped by its early-branching origins in the eukaryotic phylogeny. The methylation network in Giardia is highly reduced relative to other eukaryotes, lacking canonical arginine protein methyltransferases or demethylases and seemingly confined to six SET-like lysine protein methyltransferases. We undertook the first efforts to characterize methylation in Giardia and confirmed this unusal methylation profile in multiple seminal lines via immunoblotting, detecting mono-, di- and tri-methylation of lysine, but no arginine methylation of any known type. Immunoaffinity enrichment and mass spectrometry of lysine methylation in the infective stage (trophozoite) identified 492 methylation sites on 304 proteins, with the majority detected as mono-methylated (84.76%). Many proteins associated with the Giardia cytoskeleton, which is involved in adhesion, motility and virulence, were detected as methylated, including microtubule, motor, axoneme-associated and annexin-repeat proteins. We detected methylated helicases, ribosomal/ribonucleoproteins and histone H2 and H3 variants, suggesting a role for methylation in gene regulation, which is implicated in drug resistance. Preliminary inhibitor screening has demonstrated the methyltransferase inhibitor Chaetocin, and related idithiodiketopiperazine (ETP) analogues, inhibit trophozoites, though with lower potency than recorded in mammalian lines. Our future work aims to explore the sites and substrates of methylation in the transmissive life-stage (cyst), and the effect of methylation inhibitors on encystation (differentiation) and drug resistance.