Since their discovery a decade ago, long non-coding RNAs (lncRNAs) have emerged as a significant part of the regulatory elements in genomes. However, the role of most of them remains to be clarified. Exploring the lncRNA conservation between species is an approach for improving their annotation by inferring function in one species from another one more studied, as was previously done for protein coding genes (PCGs). However, unlike PCGs, lncRNA sequences are not well conserved across species, only by patches of a few nucleotides. Thereore, no lncRNA orthologs are reported in reference databases such as Ensembl BioMart, regardless of species, this in contrast to PCGs. A few specialized databases reported lncRNAs orthologs, such as SyntDB or NONCODEv6, which target specific species and use whole-genome alignment approaches based on syntenic regions identified with liftOver and reduced gap penalties. In this context, we have developed a workflow combining 3 methods which can be used for any species of interest: the 1st method uses a “PCG-lncRNA-PCG” triplet with 2 orthologous PCGs on either side of the lncRNA as an “anchor.” The 2nd method is based on “lncRNA-PCG” pairs with just one orthologous PCG and the lncRNA and PCG transcripts in both species must be in the same genomic orientation. Finally, the last method considers the alignment of lncRNAs but by small patches, using the “Mercator-Pecan” multiple genome alignment method. Applied on 8 species covering a broad phylogenetic scale from mammals to chicken, these 3 methods are complementary regardless of the species pair. Considering the 18,805 human lncRNAs (e!106), around 9,000 are identified with one orthologous in chicken, of which about 3,000 and 1000 orthologous lncRNA are detected by 2 and the 3 methods respectively. Several analyses based on the conservation of the co-expression network between species have been performed to improve the lncRNA annotation. The first results show interesting cases of network conservation between human and chicken. Project funded by the French ANR CE20 under ‘EFFICACE’ program.