Protists (unicellular eukaryotes) arguably account for most eukaryotic diversity and are central players in global biogeochemical cycles. Yet, our knowledge of protist diversity and ecology is still highly limited. One of the main bottlenecks is the lack of cultures for most environmental lineages, even though culturing is essential for understanding cell biology and physiology. Here we describe new approaches and culture collections for heterotrophic flagellates and provide insights about the strengths and challenges of the culturing approach.