The experimental materials of Gastrodia elata were harvested from Xiaocaoba in Yunnan Province (latitude 27.79°N longitude 104.24°E) located in the southwestern China. Genome sequencing and assembly was done on the scape of beige-scape G. elata. Five transcriptomes were sequenced from five different G. elata tissues (protocorm, juvenile tuber, immature tuber, mature tuber, scape). Four different G. elata tissues (protocorm, juvenile tuber, immature tuber, mature tuber) were collected to investigate the diversity of microbial communities. High-quality genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit.