Ramie (Boehmeria nivea (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems was grown in the soil or in a hydroponic water solution, and cultured in the same environmental conditions. Root samples of terrestrial ramie, and different developmental stages of hydroponic ramie (5 days, 30 days), were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000. Gene expression levels of each samples were quantified using the BGISEQ500 platform to help understand the distribution of aquatic root development related genes at the macro level (GSE98903). Our data resources provided an opportunity to elucidate the adaptation mechanisms of ramie seedlings roots in aquatic environment.