Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists (picoeukaryotes, 0.2-3 um). Single-cell genomics and metatranscriptomics have recently started to shed light on the biology of these uncultured organisms. Here we describe the first application of single-cell genomics to heterotrophic flagellates, focusing on the marine stramenopile MAST-4 lineage.