Ascetosporea (Rhizaria) is a group of intracellular parasites of marine invertebrates. While they cause substantial yearly losses in aquaculture, little is known about their genomes. Here, we sequenced, assembled, and decontaminated the genomes of three new Ascetosporean species: Bonamia ostreae, Marteilia pararefringens, and Paramarteilia canceri. In addition, we sequenced the Rhizarian amoeba strain M6MM. This dataset opens up new opportunities to study the biology of Ascetosporea and the evolution of parasitism in Rhizaria.