Objective Coxsackievirus A16 (CA16) is the main pathogenic pathogen of hand, foot and mouth disease (HFMD), but its pathogenic mechanism remains unclear. In this study, Genetic Diversity Mice were used to screen the pathogenic genes of CA16 and to explore the pathogenic mechanism. Methods Twenty-three strains of Genetic Diversity Mice were selected as the experimental group and C57BL/ 6 mice were used as the control group. Both groups were challenged with 10⁷ copies of CA16 by intraperitoneal injection. Blood and hind limb skeletal muscle were collected, and the viral load was detected by real-time quantitative PCR. Then, the GeneMine systems genetics database was used to analyze data of infection and to screen CA16 pathogenicity-related genes. Results Seven mouse strains and 16 genes associated with CA16 were screened from the infection data of Genetic Diversity Mice. For all seven Genetic Diversity Mice strains, the viral loads in blood and muscles tissue were all >10⁴Copie / (μL/ mg) and skeletal muscle showed significant pathological damage. Based on The GeneMine database, the pathogenicity-related genes were mainly distributed in chromosomes 3 and 4. Conclusions Genetic Diversity Mice resources provide a new method for the study of CA16 pathogenicity-related genes.