ecology and evolution. Thus, achieving a reliable delineation of cryptic species within parasitic protistan lineages is critical for gaining a better knowledge of their ecological niches and host range. The problem of species delineation is pervasive for parasitic lineages almost exclusively composed of environmental sequences, such as the Marine ALVeolate lineages (MALVs) 10,11. MALV represented one of the most hyperdiverse lineages (>1,000 OTUs) recovered in the metabarcoding dataset collected during the Tara Oceans expedition 5,12. However, only a handful of species representatives of the different MALV lineages have been formally described, all of them obligatory aplastidial parasites occurring as intracellular biotrophs (i.e., the host is maintained alive during the infection but eventually killed) and belonging to the order Syndiniales 11. Among them, Amoebophryidae (or MALV-II) were observed to have the highest rate of cladogenesis (i.e., speciation minus extinction rates) among 65 marine protist lineages 13 , making their classification even more challenging. The Amoebophrya ceratii species complex is a MALV-II clade with a worldwide distribution that can be isolated in culture 14,15. All A. ceratii reported to date were observed infecting a broad range of marine dinoflagellates 11,16. A single infected host produces within days hundreds of dinospores (i.e., free-living, flagellated infective propagules), each with a life span of few days 17. Dinospores frequently account for a substantial proportion (>25%) of the nanoplanktonic fraction (2-20 µm) in coastal waters 18 and can be readily consumed by microzooplankton grazers (20-200 µm) 19. Consequently, such parasites potentially constitute key trophic links between different compartments of the marine food web in the oceanic carbon cycle 20 , notably through population control of dinoflagellate blooms 21,22. Here, we explored the diversity of the A. ceratii species complex through an extensive sequencing effort of 76 strains in culture and 43 environmental single-cells from two close localities (the Penzé and Rance Estuaries, western Channel, France). We followed a polyphasic approach to provide the first comprehensive species boundaries delineation within the A. ceratii species complex. To do so, we combined (i) ribotyping (both of the SSU rDNA and ITS1-5.8S-ITS2 regions), (ii) k-mer analysis from whole-genome sequencing, (iii) analysis of the ITS2 compensatory base changes (CBCs), (iv) phenotypic characteristics of dinospores by flow cytometry, and (v) assessment of their host range through cross-infection culture experiments. Finally, we applied our novel species boundaries to answer the following questions: do these Amoebophrya cryptic species share the same ecological niches? Can we explain their fitness (maximal abundance and persistence in time) by their host range? For that, we explored the population dynamics of the newly-defined cryptic Amoebophrya species (considered here as ribotypes until formal descriptions are performed) during a three-year...