Hypocreomycetidae is a highly diverse group with species from various habitats. This subclass has been reported as pathogenic, endophytic, parasitic, saprobic, fungicolous, lichenicolous, algicolous, coprophilous and insect fungi from aquatic and terrestrial habitats. In this study, we focused on freshwater fungi of Hypocreomycetidae which resulted 41 fresh collections from China and Thailand. Based on morphological and phylogenetic analyses, we identified 26 species that belong to two orders (Hypocreales and Microascales) and six families (Bionectriaceae, Halosphaeriaceae, Microascaceae, Nectriaceae, Sarocladiaceae and Stachybotryaceae). Ten new species are introduced and 13 new habitats and geographic records are reported. Mariannaea superimposita, Stachybotrys chartarum and S. chlorohalonatus are recollected from freshwater habitats in China. Based on phylogenetic analysis of combined LSU, ITS, SSU, rpb2 and tef1-α sequences data, Emericellopsis is transferred to Hypocreales genera incertae sedis; Pseudoacremonium is transferred to Bionectriaceae; Sedecimiella is placed in Nectriaceae; Nautosphaeria and Tubakiella are excluded from Halosphaeriaceae and placed in Microascales genera incertae sedis; and Faurelina is excluded from Hypocreomycetidae. Varicosporella is placed under Atractium as a synonym of Atractium. In addition, phylogenetic analysis and divergence time estimates showed that Ascocodina, Campylospora, Cornuvesica and Xenodactylariaceae form distinct lineages in Hypocreomycetidae and they evolved in the family/order time frame. Hence, a new order (Xenodactylariales) and three new families (Ascocodinaceae, Campylosporaceae and Cornuvesicaceae) are introduced based on phylogenetic analysis, divergence time estimations and morphological characters. Ancestral character state analysis is performed for different habitats of Hypocreomycetidae including freshwater, marine and terrestrial taxa. The result indicates that marine and freshwater fungi evolved independently from terrestrial ancestors. The results further support those early diverging clades of this subclass, mostly comprising terrestrial taxa and freshwater and marine taxa have been secondarily derived, while the crown clade (Nectriaceae) is represented in all three habitats. The evolution of various morphological adaptations towards their habitual changes are also discussed.