RNA-Seq transcriptome data from twenty Siberian sturgeon gonads at different developmental stages is described: ten undifferentiated gonads, six gonads of immature males and four gonads from immature females. Siberian sturgeon, Acipenser baerii, is long-lived, late-maturing fish farmed in 50 countries but its production remains on a craftsman scale when compared to industrial species. Sturgeon genetic and physiological studies are less developed than for industrial fish. The data presented hereafter enables fundamental studies on the regulatory mechanisms of sturgeon gonad development, which can further be applied both in aquaculture and in fundamental research. (C) 2020 The Author(s). Published by Elsevier Inc.