In the past years, it became evident that long noncoding (lnc)RNAs have crucial roles in the developing and adult heart. These transcripts operate through diverse modes of action, including as molecular guides, scaffolds, and decoys. An important class of lncRNAs emerges from enhancer sequences. Many lncRNAs act both in Cis, nearby their site of transcription, and in Trans, at other locations in the genome, making them ideal regulators of epigenomic remodeling and genome organization. These two processes are the key determinants of lineage-specific transcriptional regulation during differentiation and cellular reprogramming. We have established therefore a pipeline for identifying relevant lncRNAs in a context of heart disease. Overall, our work supports the utility of lncRNAs as therapeutic targets for modulating cardiac cell identity and behavior in the heart. In our recent projects, we have used very deep RNA-Sequencing followed by ab initio computational transcript reconstruction, and chromatin mark assessment to identify, classify and functionally characterize lncRNAs in the heart after infarction. In addition, we combine this unique information with single-cell RNA-Sequencing to probe population heterogeneity in the normal and injured heart. Relevant cardiac subpopulations can be identified based on the sole expression of lncRNAs. Moreover, this approach allows identifying lncRNAs uniquely expressed by specific subpopulations in the damaged heart. These molecules represent attractive therapeutic targets for limiting adverse remodeling and improving function.