Endogonales (Mucoromycotina), composed of Endogonaceae and Densosporaceae, is the only known non‐Dikarya order with ectomycorrhizal members. They also form mycorrhizal‐like association with some non‐Spermatophyte plants. It has been recently proposed that Endogonales were among the earliest mycorrhizal partners with land plants. It remains unknown whether Endogonales possess genomes with mycorrhizal‐lifestyle signatures and whether Endogonales originated around the same time as land plants did.

We sampled sporocarp tissue from four Endogonaceae collections and performed shotgun genome sequencing. After binning the metagenome data, we assembled and annotated the Endogonaceae genomes. We performed comparative analysis on plant‐cell‐wall‐degrading‐enzymes (PCWDEs) and small secreted proteins (SSPs). We inferred phylogenetic placement of Endogonaceae and estimated the ages of Endogonaceae and Endogonales with expanded taxon sampling.

Endogonaceae have large genomes with high repeat content, low diversity of PCWDEs, but without elevated SSP/secretome ratios. Dating analysis estimated that Endogonaceae originated in the Permian‐Triassic boundary and Endogonales originated in the mid‐late Silurian. Mycoplasma‐related endobacterium sequences were identified in three Endogonaceae genomes.

Endogonaceae genomes possess typical signatures of mycorrhizal lifestyle. The early origin of Endogonales suggests that the mycorrhizal association between Endogonales and plants might have played an important role during the colonization of land by plants.