1 Introduction Apusomonadida is an enigmatic lineage of heterotrophic nanoflagellates (2–20 μm in size) that bear two flagella and inhabit fresh water, moist soils, and marine environments, where they glide along substrates and ingest bacteria (Heiss et al. 2015; Torruella et al. 2017). Their first records, under light microscopy only, placed them in two morphotype-defined genera: the fusiform Amastigomonas (Griessmann 1913) and the circular Apusomonas (Aléxéieff 1924).