Long non-coding RNAs (lncRNAs) are an exclusive type of ribo-regulators controlling post-transcriptional regulation in various organisms, especially in plants. Recently, important functions of long intergenic non-coding RNAs (lincRNAs), non-coding transcripts with size > 200 nts and transcribed from the intergenic regions of the genome, such as flowering, ripening, fertility, and storage organ developments were reported in plants. However, the knowledge of cassava lincRNAs in particular tissues are still limited. In this work, we aim to do genome-wide identification of lincRNAs in 11 cassava tissues, including shoot, root, and callus by using tissue-specific RNA-seq data and bioinformatics approach. Here, we showed 1,258 lincRNAs with various expression levels in cassava tissues. Of these, 67 lincRNAs were commonly  xpressed in all 11 cassava tissues and 4 of them were proposed as potential reference genes for relative gene expression quantification measurement in cassava. Moreover, 657 lincRNAs specifically expressed in single individual tissues. Cis-regulatory target prediction  uggested the potential roles of two lincRNAs involving in carbohydrate metabolism in storage roots and photosynthesis in cassava leaves. The genome-wide collection of lincRNAs in 11 specific tissues of cassava will be useful for further molecular function validation.