Significance Microsporidia are poorly treatable eukaryotic pathogens that threaten human health and industrially valuable insects and fish, yet we are only beginning to understand the complex biology of these emerging pathogens. Here we combine bioinformatics, biochemistry, and mass spectrometry analyses to show that Microsporidia carry an error-prone machinery of protein synthesis, and that their protein synthesis is accompanied by a remarkable number of translation errors. This finding reveals a previously unknown aspect of protein synthesis in these emerging parasites and creates a potential opportunity to use the defective protein synthesis machinery as a therapeutic target to treat microsporidia infections.