Long non-coding RNAs (lncRNAs) are non-translated molecules longer than 200 nucleotides that have been extensively studied in mammal genomes. Their roles are diverse, involved in chromatin modifications, transcriptional regulation, and conformational changes in proteins. However, this class of RNAs remains still largely uninvestigated in plants with few exceptions. For instance, IPS1 is a lncRNA expressed upon phosphate starvation and it is believed to counteract the activity of the miR399 on PHO2, which in turn regulates the expression of phosphate transporter genes. In Arabidopsis, the lncRNA COLDAIR was showed to be required to establish and maintain a stable silenced state of FLC by recruiting the histone methylase PRC2, thus affecting flowering time. Finally, in Medicago truncatula, the lncRNA Enod40 was showed to participate in the establishment of symbiotic interactions with soil-bacteria by affecting nodule formation. These findings highlight that lncRNA could be of great interest in plant biology and in breeding as regulating important agronomic traits. In order to deepen our understanding of the role of lncRNAs in plant biology, their comprehensive annotation is mandatory. To achieve this goal, we used a computational approach to annotate lncRNAs from RNA-seq data. Our pipeline let to distinguish lncRNA from protein-coding and other classes of non-coding RNAs, such as rRNA, precursors of miRNAs, etc. We identified thousands of putative lncRNAs using publicly available RNA-seq data in 2 monocotyledons, 7 dicotyledons, and a green algae. The identified sequences will be analyzed in order to assign a putative function and to study their conservation among different taxa. With the aim to facilitate the study of lncRNAs for the plant research community, we present the Green Non-Coding Database (GreeNC) that will provide information about sequence, expression levels, genomic context, ontology and phylogeny of lncRNAs in plants.