Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and cold-stress related expression of lncRNAs in tilapia is still limited. Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 126 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 35,328 high-confidence set of lncRNAs were detected from the RNA-seq datasets. 5,939 lncRNAs (~17%) were overlapped with 13,450 mRNA genes with at least one basepair of overlap. We observed an average correlation coefficient of 0.06 for all lncRNA-mRNA pairs, 0.09 for lncRNA-lncRNA pairs and 0.12 for mRNA-mRNA pairs. These correlation data is far less than that for the overlapped lncRNA and mRNA pairs (r = 0.22). Weighted correlation network analysis of the lncRNA and mRNA datasets from 14 tissues identified 30 modules and many interesting genes existed, e.g., SLC13A1, GGT1, GRHL1, GATA3, RE11, CLDN4L, CLDN8, OCLN. Differential expression (DE) analysis identified 923 and 246 DE lncRNAs in brain and heart, respectively. miRNA-lncRNA interaction analysis detected 923 lncRNAs containing motifs with sequence complementary to 462 miRNAs in brain, and 246 lncRNAs showing interaction with 462 miRNAs in heart. This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will elucidate their roles in regulating stress-related adaptation.