Currently available microbial genomes are of limited phylogenetic breadth due to ourhistorical inability to cultivate most microorganisms in the laboratory. The firstphase of the Microbial Dark Matter project used single-cell genomics to sequence 201single cells from uncultivated lineages, and was able to resolve new superphyla andreveal novel metabolic features in bacteria and archaea. However, many fundamentalquestions about the evolution and function of microbes remain unanswered, and manycandidate phyla remain uncharacterized. Phase II of the Microbial Dark Matter projectwill target candidate phyla with no sequenced representatives at a variety of new sites usinga combination of single-cell sequencing and shotgun metagenomics approaches.