Mitosomes are highly divergent, often reduced, mitochondrion-derived organelles. Mitosomes in Entamoeba histolytica possess a unique metabolic role that has not been discovered in other eukaryotes. Sulfate activation, in which sulfate is activated with two ATP molecules to form 3′-phosphoadenosine-5′-phosphosulfate, is compartmentalized in Entamoeba mitosomes. Sulfate activation is essential for the production of sulfur-containing polar lipids and proliferation of trophozoites. Besides its unique metabolic role, the mechanisms of protein and solute transport across mitosomal double membranes are also highly divergent from other eukaryotes. For instance, the translocator of the outer membrane consists of the β-barrel pore component Tom40 and the unique peripheral membrane component Tom60, the latter of which is localized to both the mitosomal outer membrane and the cytoplasm and functions as a shuttle carrier of mitosomal proteins. In this chapter, we summarize the discovery, functions, and protein transport of Entamoeba mitosomes, and also discuss remaining important biochemical and biological riddles of mitosomes, including other metabolic functions, redox control, regulation of gene expression, solute/metabolite transport, replication, and degradation.