To date, the main focus of the sequencing revolution has been on a limited set of eukaryotes, mostly consisting of animals, plants, fungi and their parasites. However, the vast majority of eukaryotic diversity is microbial and free-living and to fully appreciate the path to parasitism we need to sample the genomes of these organisms. We seek to obtain genome information from a diverse set of poorly sampled organism groups, some of which are related to significant parasites in humans and animals. To this end, we have established nanopore sequencing as powerful tool to obtain near-complete genome sequences of a varied set of microbial eukaryotes grown in prokaryotic co-cultures. Long-read sequence assemblies in combination with polyA-selected RNAseq data have proven to be a powerful tool to enable accurate taxonomic binning of eukaryotic genomes from complex starting cultures.