•Fungi have essential functions in plant health and performance. However, the plant-associated functions of many cultured fungi have not been established in detail. • Here, the fungal species diversity of the Salvia miltiorrhiza root and rhizosphere were first obtained by culturomics and high-throughput sequencing. In addition, we present a comprehensive functional metagenomic analysis of the cultured fungi, and agar plates verified the activities of cellulase and chitinase predicted by metagenomic. • We first present a collection of cultured fungi from the root and rhizosphere of Salvia miltiorrhiza, including 92 species across 37 families and 5 phyla, Ascomycota was the dominant species. Many rDNA internal transcribed spacer sequences were unassigned at lower taxonomic levels. 19 genera of endophytic fungi and 37 genera of rhizosphere fungi are first reported. The cultivation-dependent approach demonstrated a lower taxonomic diversity than high throughput sequencing, but some fungi existed only in cultures. Structural analyses indicated that the dominant species differed in cultured and noncultured samples at other levels except for the phylum level. Functional analysis showed that 223 carbohydrate enzyme families and 393 pathway maps were identified in the CAZy and KEGG databases, respectively. The most abundant families were glycoside hydrolases and carbohydrate metabolism. As predicted by metagenomics, we experimentally verified cellulase and chitinase activities for 29 and 74 fungi, respectively. •We provide the first evidence for biomass recycling by fungi associated with plants. Culturing is necessary to decipher the hidden microbial community and the critical functions in plant-microbe interactions.