Here, we first systematically identified and characterized responsive lncRNAs and mRNAs expressed in leaves of sugar beet at a genome-wide scale, focusing on alkaline-responsive lncRNAs and mRNAs. Overall design: Five-week-old seedlings were treated with Hoagland solution, containing 75 mM mixed alkaline solution (Na2CO3:NaHCO3, 1:2) for 0 day (control, designated as C), 3 days (short-term treatment, designated as ST) and 7 days (long-term treatment, designated as LT). Fresh leaves from the same position of seedlings at different treatments were collected, and three biological replicates were sampled.