Clade 1 Harzianum

• 11atrog Hypocrea atrogelatinosa
• 11cat Hypocrea catoptron/Trichoderma catoptron
• 11cinn Hypocrea cinnamomea/Trichoderma cinnamomeum
• 11harz Hypocrea lixii/Trichoderma harzianum
• 11WJ608 Hypocrea sp. WJ 2608
• 11WJ2701 Hypocrea sp. WJ 2701
• 11stram Hypocrea straminea/Trichoderma stramineum
• 11tawa Hypocrea tawa
• 11thail Hypocrea thailandica/Trichoderma thailandicum
• 11aggr Trichoderma aggressivum
• 11cer Trichoderma cerinum
• 11cfaur Trichoderma pleuroticola
• 11pleuro Trichoderma pleurotum
• 11tom Trichoderma tomentosum
• 11vel Trichoderma velutinum

Clade 2 Virens

• 12cras Hypocrea crassa/Trichoderma crassum
• 12viren Hypocrea virens/Trichoderma virens

Clade 3 Semiorbis

• 13hun Hypocrea hunua
• 13sem Hypocrea semiorbis
• 13fert Trichoderma fertile
• 13obl Trichoderma oblongisporum

Clade 4 Strictipilis

• 14aurM Hypocrea aureoviridis var. macrospora
• 14cun Hypocrea cuneispora
• 14stric Hypocrea strictipilosa/Trichoderma strictipilis
• 14longip Trichoderma longipile

Clade 5 Stromaticum

• 15ross Trichoderma rossicum
• 15_3559 Trichoderma sp. PPRI 3559
• 15strom Trichoderma stromaticum

Clade 9 Pachybasioides

• 19lacu Hypocrea lacuwombatensis
• 19minu Hypocrea minutispora/Trichoderma minutisporum
• 19poly Hypocrea pachybasioides/Trichoderma polysporum
• 19parap Hypocrea parapilulifera
• 19pilu Hypocrea pilulifera/Trichoderma piluliferum
• 19stel Hypocrea stellata

Clade 14 Longibrachiatum

• 214andi Hypocrea andinensis
• 214cerebr Hypocrea cerebriformis
• 214jecor Hypocrea jecorina/Trichoderma reesei
• 214nov Hypocrea novaezelandiae
• 214orien Hypocrea orientalis
• 214patel Hypocrea patella
• 214poron Hypocrea poronoidea
• 214pseud Hypocrea pseudokoningii/Trichoderma pseudokoningii
• 214citrinv Hypocrea schweinitzii/Trichoderma citrinoviride
• 214effu Trichoderma effusum
• 214ghane Trichoderma ghanense
• 214konil Trichoderma konilangbra
• 214longib Trichoderma longibrachiatum
• 214satur Trichoderma saturnisporum
• 214sin Trichoderma sinensis
• 214_3642 Trichoderma sp. MA 3642

Clade 12 Viride

• 412atro Hypocrea atroviridis/Trichoderma atroviride
• 412kon Hypocrea koningii/Trichoderma koningii
• 412muri Hypocrea muroiana
• 412virid Hypocrea rufa/Trichoderma viride
• 412stilb Hypocrea stilbohypoxyli
• 412vididsc Hypocrea viridescens/Trichoderma viridescens
• 412aust Trichoderma austrokoningii
• 412a_caribbae Trichoderma caribbaeum var. aequatoriale
• 412carib Trichoderma caribbaeum var. caribbaeum
• 412ding Trichoderma dingleyeae
• 412dorot Trichoderma dorotheae
• 412erin Trichoderma erinaceum
• 412intr Trichoderma intricatum
• 412kons Trichoderma koningiopsis
• 412ova Trichoderma ovalisporum
• 412peter Trichoderma petersenii
• 412rog Trichoderma rogersonii
• 412strig Trichoderma strigosum
• 412taiw Trichoderma taiwanense

Clade 13 Pachybasium "A" or Hamatum

• 413flav Hypocrea flaviconidia
• 413neor Hypocrea neorufa
• 413pez Hypocrea pezizoides
• 413asper Trichoderma asperellum
• 413ham Trichoderma hamatum
• 413pub Trichoderma pubescens
• 413theob Trichoderma theobromicola

Clade 7 Ceramica

• 57ceram Hypocrea ceramica/Trichoderma ceramicum
• 57est Hypocrea estonica/Trichoderma estonicum

Clade 8 Chlorospora

• 58aure Hypocrea aureoviridis/Trichoderma aureoviride
• 58cand Hypocrea candida/Trichoderma candidum
• 58chlo Hypocrea chlorospora/Trichoderma chlorosporum
• 58cost Hypocrea costaricensis
• 58crem Hypocrea cremea/Trichoderma cremeum
• 58sinu Hypocrea sinuosa/Trichoderma sinuosum
• 58surr Hypocrea surrotunda/Trichoderma surrotundum
• 58thele Hypocrea thelephoricola/Trichoderma thelephoricolum
• 58viresc Hypocrea virescentiflava

Clade 10 Psychrophyla

• 510megal Hypocrea megalosulphurea

Clade 16 Megalocitrina

• 516cryst Hypocrea crystalligena
• 516psy Hypocrea psychrophila
• 516pulv Hypocrea pulvinata
• 516sulph Hypocrea sulfurea

Clade 17 Citrina

• 517citr Hypocrea citrina

Clade 6 Lutea

• 56lut Hypocrea lutea
• 56mela Hypocrea melanomagnum
• 56brev Trichoderma brevicompactum

Clade 11 Lone lineages

• 611chrom Hypocrea chromosperma/Trichoderma chromospermum
• 611gela Hypocrea gelatinosa/Trichoderma gelatinosus
• 611nigrov Hypocrea nigrovirens
• 611phyll Hypocrea phyllostachydis/Trichoderma phyllostahydis
• 611sulw Hypocrea sulawesensis
• 611vogl Hypocrea voglmayrii
• 611hel Trichoderma helicum
• 611spir Trichoderma spirale