This study unveils the microbial dark matter of soils by reconstructing 40,039 metagenome-assembled genome bins from 3304 soil metagenomes, identifying 16,530 novel species-level genome bins (uSGBs). These uSGBs enhance our understanding of microbial diversity, functional roles, and genome diversity, contributing to a vast repository of biosynthetic gene clusters and unexplored viral-host associations, with the SMAG catalogue serving as a key resource for future research.