Fish coloration has long been a scientific research hotspot, owing not only to complex biological mechanisms associated with the prominent phenotypic characteristics, but also to high evolutionary significance for adaptation. Lately, an increasing number of researches have focused on lncRNA, due to their involvement in biological regulatory function. However, studies on lncRNAs in non-model organism such as Cynoglossus semilaevis are still lacking, particularly on skin melanostic mechanism. C. semilaevis is an important farmed marine fish in China and is easy to present the melanistic problem of blind side skin in the process of artificial cultivation. The blind side pigment abnormalities would spread with varying degrees of areas. It has not been known how pigment is correctly transported to the corresponding skin in C. semilaevis so far. In order to investigate the blind side melanized mechanism of lncRNA and mRNA in C. semilaevi, this experiment predicted that lnc-XR_003049606.1 targets pmelb through trans-acting according to the results of the transcriptome analysis. Bioinformatics analysis revealed that the full length of the cDNA of pmelb was 1 755 bp, encoding 584 amino acids, with a predicted protein molecular weight of 63.94 ku and a theoretical isoelectric point of 5.12. The predicted secondary protein structure contains a Pleckstrin homology domain, a Bruton's tyrosine kinase Cys-rich motif, a Src homology 3 domains, a Src homology 2 domains and a tyrosine kinase catalytic domain. Phylogenetic tree analysis showed that pmelb was clustered with corresponding genes in other fishes. The amino acid homology analysis showed that pmelb had the highest similarity with Scophthalmus maximus and Paralichthys olivaceus (68.05% and 66.28%, respectively). Analysis of the spatio-temporal expression patterns on lnc-XR_003049606.1 and pmelb revealed that lnc-XR_003049606.1 was expressed in the skin and liver of 1-year-old tongue sole, with expression peaking in the skin at 60 days and then decreasing over time, whereas pmelb was mainly expressed in the skin, with expression increasing and then decreasing over the timeline. This study provided an idea for further screening the key genes that play a role in the process of blind side hypermelanotic skin in C. semilaevi.