Antimicrobial drugs used in bacterial infections exploit the differences in cell biology between prokaryotic and eukaryotic cells to target the bacterial pathogen, while its host remains largely unaffected. Infections caused by eukaryotic pathogens, such as parasitic protozoa, are often more difficult to treat due to the highly similar cell biology between the pathogen and its eukaryotic host. This complication could be overcome by searching the genomes of parasitic protozoa for genes that are: 1) important for cell growth or virulence 2) absent from the genome of their host and 3) of bacterial origin. We have identified two gene families encoding tRNA modification enzymes in several eukaryotic microbes, which were acquired from the Chlamydiae family of obligate intracellular bacteria via horizontal gene transfer. These proteins localise to various compartments of the cell including the mitochondrion, chloroplast and endoplasmic reticulum. Among the eukaryotic microbes that possess these bacterial proteins are the oyster pathogen Perkinsus marinus as well as the clinically-relevant human pathogens Entamoeba histolytica and Acanthamoeba castellanii. The chemical modifications catalysed by tRNA modification enzymes are important for tRNA function, translation efficiency and in some cases virulence. The bacterial origin and horizontal acquisition of these enzymes also means they are absent in their respective hosts. Taken together, these horizontally acquired enzymes have potential for the development of drugs that inhibit their activity with no effect on the host. We hypothesise that the development of inhibitors that specifically target these enzymes may lead to novel strategies to treat or slow the progression of E. histolytica and A. castellanii infections as well as provide significant economic savings for oyster farms that are plagued by P. marinus. Thus, prokaryote-to-eukaryote horizontal gene transfer represents an untapped resource of potential drug targets in pathogenic eukaryotes.