Eukaryotic microorganisms from diverse environments encompass a large number of taxa, many of them still unknown to science. One strategy to mine these organisms for genes of biotechnological relevance is to use a pool of eukaryotic mRNA directly extracted from environmental samples. Recent reports demonstrate that the resulting metatranscriptomic cDNA libraries can be screened by expression in yeast for a wide range of genes and functions from many of the different eukaryotic taxa. In combination with novel emerging high-throughput technologies, we anticipate that this approach should contribute to exploring the functional diversity of the eukaryotic microbiota. Microbial Eukarya represent an underexplored source of biocatalysts and metabolites. Metatranscriptomics based on the utilization of mRNA extracted from environmental samples represents a suitable approach to mine the environmental eukaryotic gene pool for genes relevant to biotechnology. cDNAs derived from soil-extracted poly-A mRNA have been expressed in yeast. These genes, which encode functional intracellular, membrane, or extracellular proteins, originate from unrelated eukaryotic taxa, some of unknown affiliation. Several of these genes define novel gene families, thus highlighting the potential of this protocol to explore the eukaryotic gene space. We anticipate that emerging experimental approaches such as sequence capture by hybridization or high-throughput screening by droplet microfluidics should provide a decisive contribution to this emerging research field.