Aphelids remain poorly known parasitoids of algae and have recently raised considerable interest due to their phylogenetic position at the base of Fungi. Accordingly, aphelids may still display some ancestral characters that were subsequently lost in the fungal lineage. Some mycologists consider the aphelids as Fungi. However, unlike Fungi, they are phagotrophs. Molecular environmental studies have revealed a huge diversity of aphelids, but only four genera have been described: Aphelidium, Amoeboaphelidium, Paraphelidium and Pseudaphelidium. Studying new freshwater aphelid strains by molecular, light and electron microscopy methods, we identified a new aphelid species, Aphelidium insulamus. Molecular phylogenetic analysis of the 18S rRNA gene indicates that it is sister to Aph. melosirae and, together with Aph. tribonematis, they form a monophyletic cluster, which is distantly related to both Paraphelidium, with flagellated zoospores, and Amoebaphelidium, with amoeboid zoospores. Ultrastructure of all main life-cycle stages revealed new data for Aphelida cell biology: zoospores and their kinetid (flagellar apparatus) structure, plasmodium, and resting spore. We present the molecular phylogeny of these aphelids using Chytridiomycota as an outgroup.