Screening strategies for anti-tuberculosis compounds using Mycobacterium tuberculosis are time-consuming and require BSL-3 facilities, which makes the development of high-throughput assays difficult and expensive. Mycobacterium marinum, a close genetic relative of M. tuberculosis, possesses several advantages as a suitable model for tuberculosis drug screening. However, despite the high genetic similarity, there are some obvious differences in susceptibility to some tuberculosis drugs between these two species, especially for the pro-drugs ethionamide and isoniazid. In this study, we aimed to improve M. marinum as a model for anti-tuberculosis drugs identification by heterologous expression of two common drug activators, EthA and KatG. These two activators were overexpressed in M. marinum and the strains were tested against ethionamide, isoniazid and a library of established antimycobacterial compounds from TbAlliance to compare drug susceptibility. Both in vitro and in vivo using zebrafish larvae, these genetically-modified M. marinum strains showed significantly higher susceptibility against ethionamide and isoniazid, which require activation by EthA and KatG. More importantly, a strain overexpressing both ethA and katG was potentially more susceptible to approximately 20% of the anti-tuberculosis hit compounds from the TB Alliance library. Most of these compounds were activated by EthA in M. marinum. Four of these compounds were selected for further analysis and three of them showed obvious EthA-dependent activity against M. tuberculosis. Overall, our developed M. marinum strains are valuable tools for high-throughput discovery of potential novel anti-tuberculosis pro-drugs.