Background: Agrocybe aegerita, the black poplar mushroom, has been highly valued as a functional food for its medical and nutritional benefits.Several bioactive extracts from A.aegerita have been found to exhibit antitumor and antioxidant activities.However, limited genetic resources for A.aegerita has hindered exploration of this species.Methodology/Results: To facilitate the research on A.aegerita, we compared genome-wide transcriptional and proteome-wide translational changes between mycelium and fruiting body.We applied high-throughput sequencing technology (Illumina) to sequence A.aegerita transcriptomes from mycelium and fruiting body.The raw clean reads were de novo assembled into a total of 36,134 unigenes with an average length of 663 bp.These unigenes were annotated and classified according to gene ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways.Gene expression profile analysis showed that 18,474 unigenes were differentially expressed, with 10,131 up-regulated in mycelium and 8,343 up-regulated in fruiting body.And we randomly selected some genes to comfirm their altered expression levels by semi-quantitative RT-PCR.Based on one-dimensional gel electrophoresis (1-DGE)coupled with electrospray ionization liquid chromatography tandem MS (LC-ESI-MS/MS), we identified 222 (197 non-redundant proteins) and 238 (213non-redundant proteins) proteins from mycelium and fruiting body, respectively.GO annotation was performed to better understand the functions of these proteins.The global comparison of transcriptomic and proteomic data highlighted the importance of carbohydrate and amino acid metabolism during the development ofA.aegerita.Conclusion: This is the first study on transcriptome and proteome analyses of A.aegerita.This work provides important information on A.aegerita development and metabolism, and offers clues to the applications of this mushroom in nutrition,pharmacy and industry.