Abstract: Glass catfish (Kryptopterus vitreolus) is a popular aquarium fish due to its extremely transparent body pattern. Its main body loses most of the reflective iridophores and light-absorbing melanophores, although its face and head retain certain black and iridescent iridophores. So far, molecular mechanisms of this transparent phenotype have been largely unknown yet. To identify some potential genetic clues to this fascinated transparence, we constructed a chromosome-level haplotypic genome assembly for the glass catfish with 32 chromosomes and 23,344 protein-coding genes by integration of PacBio and Hi-C sequencing technologies and a series of standard assembly and annotation pipelines. Meanwhile, we identified a premature stop codon in the putative albinism-related tyrp1b gene (encoding tyrosinase-related protein 1), thereby leading it to be a nonfunctional pseudogene. Interestingly, we also identified loss of endothelin-3 (edn3b) gene in the glass catfish genome by synteny comparison with over 30 other fish species. We then generated edn3b-/- mutant zebrafish and observed a remarkable decrease of black pigments in body surface stripes when compared to the wild zebrafish. That is to say, the loss of edn3b gene was validated to make contribution in part to the transparent phenotype of glass catfish. We established a high-quality chromosome-scale genome assembly for glass catfish, as well as identified several important genes with molecular clues to the transparent phenotype. Our current findings not only enhance our understanding of the molecular mechanisms of the transparent phenotype of glass catfish, but also offer a valuable genetic resource for in-depth investigations on pigmentation of various animals.