The conservation of long noncoding RNA (lncRNA), including primary structure, spatial structure, transcriptional position, splicing mode and tissue distribution, is research focus of lncRNA research. In-depth studies of lncRNA conservation can be applied to the screening process of lncRNA in non-modal organisms, which lack adequate reference genome databases, greatly enhancing the integrity and accuracy of lncRNA databases of non-modal organisms. LncRNA screening tools or processes such as CPC and pipeline for lncRNA annotation from RNA-seq data (PLAR), which have been developed by length of open reading frame, distribution and frequency of codon, functional domain and other conservative information, are new strategies for the screening of lncRNA and construction of reference database of non-model organisms. In this review, we summarized the conservation of lncRNA and its application in screening lncRNA in non-model organisms, and briefly introduced PLAR, a new screening method using the conservation of lncRNA.