Heterotrophic flagellates are fundamental in marine microbial food webs. They play a key role in channeling bacteria to higher trophic levels as well as in nutrient recycling. Despite this recognized ecological importance, and contrasting with the significant advances achieved with marine bacteria and archaea, little is known on the diversity of marine heterotrophic flagellates. This heterogeneous group of cells is weakly captured by microscopic and culturing approaches, and has been only recently targeted by environmental molecular surveys. This thesis is about the study of the ecology of one specific uncultured lineage, the MAST-4 (Marine Stramenopiles clade-4) group, which can be viewed as a model heterotrophic flagellate. MAST-4 consists of tiny cells (2-3 μm) that are widely distributed in the photic zone of the oceans with temperatures above ~5°C. On average, it accounts for ~9% of marine heterotrophic flagellates. It actively grazes on bacteria and other picosized cells being well adapted to the typical bacterioplankton abundances and preferring bacteria in a good physiological state. MAST-4 displays low genetic variability, being formed by just five main clades, each representing at least one biological species. This indicates that this successful group has suffered low evolutionary diversification. The most represented MAST-4 clades did not reveal geographical barriers, whereas temperature was the main factor influencing the distribution patterns. Different clades of MAST-4 seemed to have physiological adaptations that allowed them to establish and dominate under different environmental regimes. This ecotypic differentiation could partly explain the success of this flagellate, at the level of global distribution and abundance, allowing it to exploit the whole spectrum of habitat variability