Gobiopterus lacustris is a kind of small fish with strong adaptability to salinity and easy to raise in laboratory. It is an ideal model organism and environmental indicator species, whose body is transparent and its organs can be seen through naked eyes. In order to explore the cause of the transparent body color of G. lacustris, the transcriptome analysis of skin and eye of G. lacustris was carried out. A total of 103 686 unigenes were obtained by de novo splicing. The N50 and average length were 1 456 and 2 490 bp, respectively. In Nr, Nt, KO, SwissProt, PFAM, GO and KOG databases, 57 380, 37 343, 31 700, 51 277, 47 020, 47 555 and 25 604 unigenes were annotated respectively. KEGG enrichment showed that tyr, tyrp1 and tyrp2 were significantly down regulated in melanin production pathway. In addition, the results showed that there were 8 113 differentially expressed genes (DEGs) in the skin and eyes of G. lacustris, of which 3 174 were up-regulated in the skin and 4 939 in the eyes. The verification of 10 DEGs by qPCR confirmed that the RNA-Seq analysis was correct. This study enriches the body color research of G. lacustris, provides data for the utilization of G. lacustris genetic resources, and also provides a reference for further study on the formation mechanism of gorgeous body color of fish.