Our knowledge of the fungal tree of life is biased towards model systems, fungi in biotechnology applications and pathogens, thus limiting our understanding of fungal evolution and their biosynthetic diversity. Now, Ahrendt et al. use single-cell genomics to expand the fungal tree of life. The authors sequenced the genomes of eight uncultured fungi from across the fungal tree of life, focusing primarily on early-diverging fungi from the Cryptomycota, Chytridiomycota and Zoopagomycota, which represent understudied fungal taxa. Each single amplified genome of the early-diverging lineages was placed within the tree of life, and the observed high number of heterozygous genomes at the base of the fungal tree led the authors to infer a diploid (or higher aneuploidy) ancestor of fungi. They also observed metabolic deficiencies and expansions that correlate with their parasitic nature and unculturability.