To assess whether bone homeostasis in O. mykiss scales is affected by salinity changes, we used the Illumina sequencing platform to detect the overall lncRNAs expression in O. mykiss scales under different salinity acclimation times, screened DE lncRNAs, and identified classification annotation of DE lncRNAs and functional enrichment analysis of related target genes based on GO annotation and KEGG pathway enrichment analysis to identify novel calcium regulators or bone homeostasis factors.