As an efficient strategy for gene isolation, map-based cloning has been widely applied and well advanced in crops with small genomes. However, the application of this strategy is challenging in crops with large genomes that are rich in repetitive DNA. Because of the importance of map-based cloning, its basic contents and development are summarized. In particular, the application of this strategy is analyzed and evaluated in large genome crops, and the potential directions of its development are discussed. These help to promote genes cloning in large genome crops.