Ethnic minority settlements are an essential spatial carrier of regional cultural heritage. The interpretation of their landscape genes is an important measure to protect the cultural landscape of traditional settlements. Taking Zhaoxing Dong Village in Guizhou as an example, based on the theory and method of landscape gene, this study constructs the identification framework of landscape gene information chain in Dong Village, analyzes its constituent elements and characteristics, and puts forward the protection strategy of settlement landscape gene. The results show that: (1) Zhaoxing Dong Village landscape genes are subdivided into the overall layout, Dong Village buildings, landscape environment, institutional beliefs, traditional crafts, and folk culture genes. (2) The landscape gene information chain of Zhaoxing Dong Village belongs to the typical clan bond type in functional attributes and forms a branch spatial structure in morphological structure. The landscape elements are evenly distributed and belong to the core-periphery type. (3) Zhaoxing Dong Village landscape gene protection strategy is: to review and repair the Dong Village landscape mutation genes, determine the Dong Village landscape information corridor, innovative Dong Village tourism experience development model. From the perspective of landscape genes, the characteristics of the cultural landscape of Zhaoxing Dong Village are fully excavated to provide guidance for the subsequent settlement landscape protection and tourism development and construction.