lncRNAs play vital roles in cellular pathways involved in developmental and a/biotics tress response pathways. In this study, we analyzed RNA-sequencing data from 6tissues of hexaploid wheat collected in various stages of plant development, and also from drought-treated and irrigated hexaploid wheat, in order to identify lncRNA contents in these transcriptomes in silico. We performed a second in silico lncRNA identification using tetraploid wheat transcriptome and compared the results with hexaploid wheat lncRNA content to reveal similarities and differences in lncRNA characteristics and distribution among genomes. Moreover, we have looked for significantly different expression patterns of lncRNAs between irrigated and drought-treated conditions and found37 lncRNAs differentially expressed in response to mild and severe drought stress. As miRNAs involve in regulation of lncRNAs by targeting and titrating them in cellular environment, we have checked potential lncRNA-miRNA interactions as well as coding targets of those miRNAs to obtain lncRNA-miRNA-mRNA networks and to gain more insight about cellular pathways activated upon drought stress. Notably, miRNA partners of differentially expressed lncRNAs targeted a high number of transcripts coding for drought stress-related proteins such as MYB and dehydration responsive factors. Comparison of tetraploid and hexaploid lncRNA and network analysis were also performed. These findings may give a broader insight about the roles of lncRNAs in plant development and stress responses and pave the way for further studies leading to utilization of lncRNAs in molecular breeding.