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Zebrafish (Danio rerio) is an alternative model system for drug screening, developing new products, and assessing ecotoxic effects of pollutants and biomonitor species in environmental risk assessment. However, the history and current use of transgenic zebrafish lines in ecotoxicology and toxicology studies remain poorly explored. Thus, the present study aimed to summarize and discuss the existing data in the literature about the applications of transgenic zebrafish lines in ecotoxicology and toxicology. The articles were analyzed according to publication year, journal, geographic distribution, and collaborations. Also, the bioassays were evaluated according to the tested chemical, transgenic lines, development stage, biomarkers, and exposure conditions (i.e., concentration, time, type, and route of exposure). Revised data showed that constitutive transgenic lines are the main type of transgenic used in the studies, besides most of uses embryos and larvae under static conditions. Tg(fli1: EGFP) was the main transgenic line, while the GFP and EGFP were the main reporter proteins. Transgenic zebrafish stands out in assessing vasotoxicity, neurotoxicity, systemic toxicity, hepatoxicity, endocrine disruption, cardiotoxicity, immunotoxicity, hematotoxicity, ototoxicity, and pancreotoxicity. This review showed that transgenic zebrafish lines are emerging as a suitable in vivo model system for assessing the mechanism of action and toxicity of chemicals and new biotechnology products, and the effects of traditional and emerging pollutants.