Trichoderma spp. represent one of the most important fungal genera to mankind and in natural environments. The genus harbors prolific producers of wood-decaying enzymes, biocontrol agents against plant pathogens, plant-growth-promoting biofertilizers, as well as model organisms for studying fungal-plant-plant pathogen interactions. Pursuing highly accurate, contiguous, and chromosome-level reference genomes has become a primary goal of fungal research communities. Here, we report the chromosome-level genomic sequences and whole-genome annotation data sets of four strains used as biocontrol agents or biofertilizers ( Gv29-8, FT-333, FT-101, and P1). Our results provide comprehensive categorization, correct positioning, and evolutionary detail of both nuclear and mitochondrial genomes, including telomeres, AT-rich blocks, centromeres, transposons, mating-type loci, nuclear-encoded mitochondrial sequences, as well as many new secondary metabolic and carbohydrate-active enzyme gene clusters. We have also identified evolutionarily conserved core genes contributing to plant-fungal interactions, as well as variations potentially linked to key behavioral traits such as sex, genome defense, secondary metabolism, and mycoparasitism. The genomic resources we provide herein significantly extend our knowledge not only of this economically important fungal genus, but also fungal evolution and basic biology in general. Telomere-to-telomere and gapless reference genome assemblies are necessary to ensure that all genomic variants are studied and discovered, including centromeres, telomeres, AT-rich blocks, mating type loci, biosynthetic, and metabolic gene clusters. Here, we applied long-range sequencing technologies to determine the near-completed genome sequences of four widely used biocontrol agents or biofertilizers: Gv29-8 and FT-333, FT-101, and P1. Like those of three Trichoderma reesei wild isolates QM6a, CBS999.97( ) and CBS999.97( ) we reported previously, these four biocontrol agent genomes each contain seven nuclear chromosomes and a circular mitochondrial genome. Substantial intraspecies and intragenus diversities are also discovered, including single nucleotide polymorphisms, chromosome shuffling, as well as genomic relics derived from historical transposition events and repeat-induced point (RIP) mutations.