Abstract: 【Objective】 To explore the relationship between genetic diversity and resistance to AeromonA. hydrophila in Yellow River carp(Cyprinus carpio) based on SCoT molecular markers, so as to provide a theoretical basis for breeding for disease-resistant in C. carpio.【Method】 300 C. carpio were infected with A. hydrophila through intraperitoneal injection, and divided into the first dead population(FP), the last dead population(LP) and the surviving population(SP) according to the time order of mortality, with 30 carps selected from each population. The primers with high polymorphism, high repeatability and clear bands were screened from 80 SCoT primers to conduct polymorphic amplification for the 3 populations of C. carpio. The number of alleles(Na), effective alleles(Ne), Nei's gene diversity index(H) and Shannon's diversity index(I) of the 3 populations were calculated by PopGene32 and Arlequin 3.1. Phylogenetic trees were constructed based on Nei's genetic distance(Ds) using unweighted group average(UPGMA) in MEGA 7.0, and Structure 2.3 was used to analyze the genetic structure among populations.【Result】 C. carpio mortality rate infected with A. hydrophila was 40%. 18 primers with clear bands and high polymorphism were screened from 80 SCoT primers, and polymorphism from the 3 C. carpio populations. 97 polymorphic bands accounted for 94.17% of the total bands. Na ranged from 1.7961 to 1.8155, Ne ranged from 1.3828 to 1.4029, H ranged from 0.2258 to 0.2467, and I ranged from 0.3453 to 0.3804 for the 3 C. carpio populations. The genetic differentiation index(Gst) between populations was 0.0972, indicating that 90.28% of genetic diversity was distributed within the population. The genetic differentiation index(Fst) of the 3 C. carpio populations was 0.1299, indicating a mildly genetic differentiation;the Ds distribution among populations ranged from 0.0248 to 0.0835, with the greatest genetic distance between the FP and SP. The results of UPGMA clustering analysis based on Ds showed that FP and LP clustered into one branch, and SP was an independent branch. Genetic structure analysis showed that 3 C. carpio populations were divided into 2 subpopulationsdisease-resistant population(SP) and susceptible populations(FP and LP). The result of C. carpio population division according to time order of mortality were basically consistent with the results of population division by cluster analysis and genetic structure analysis.【Conclusion】 The resistance of C. carpio to A. hydrophlia grows as population genetic diversity grows. Therefore, sufficient population size should be ensured during the selection and breeding of disease-resistant C. carpio strains to ensure a certain level of genetic heterozygosity while improving other economic traits such as growth and nutrition.