Long non-coding RNA (lncRNA) are common elements in vertebrates and other lesser organisms that possess numerous regulatory and cellular roles. lncRNA are well characterized in humans and mice, however in other species, there is comparatively little information. Identifying lncRNA in bovine could aid in identifying additional sites in the genome where mutations are likely to contribute to variation in complex traits along with understanding their evolutionary importance. This is important in bovine, since genomic predictions are increasingly used for genetic improvement of milk and meat production. We address the main challenge in identifying lncRNA, namely distinguishing lncRNA transcripts from unannotated genes, by developing a strict lncRNA filtering pipeline. Our aim was to identify and annotate novel long non coding RNA transcripts in the bovine genome captured from RNA Sequencing (RNA-Seq) data across 18 tissues, sampled in triplicate.We find 9,886 transcripts passed the pipeline and show moderate to high expression. Further we find many unique lncRNA transcripts are downregulated in a tissue specific manner. This study also identified a large number of novel unknown transcripts in the bovine genome, many having high protein coding potential, indicating a clear need for better annotations of protein coding genes in the bovine genome.