【Objective】 To perform whole genome resequencing of jugular vein blood of Kazakh horses to identify candidate genes regulating differences in lactation in Kazakh horses and to provide data support for the selection of Kazakh horses for dairy performance. 【Methods】 According to the lactation volume data of 30-105 d of test horses, 12 healthy Kazakh horses with similar age, parity and consistent feeding background, that was, 6 in the high lactation group (HW) and 6 in the low lactation group were selected. Altogether, a total of 288 blood samples were collected during the whole monitoring cycle, and 48 blood samples were selected for whole genome resequencing, 6 blood samples of lactation greater than 2. 26 kg in the HW group and 6 blood samples of lactation less than 1.05 kg in the LW group were selected for whole genome resequencing, and a total of 288 blood samples were obtained. A total of 88 blood samples were collected during the whole monitoring period, and 48 blood samples were collected at the actual peak lactation date. 6 blood samples from the HW group with lactation greater than 2.26 kg and 6 blood samples from the LW group with lactation less than 1.05 kg were selected for whole-genome resequencing, which yielded a total of 20,234,241 mutated sites; 980,491,918 valid sites were obtained after removing the sequences with junctions and low-quality sequences. The loci in the first 0.000,01 of Top were selected, and the threshold value was determined to be 0.000,147,8, with a total of 88 mutation loci located in 40 candidate genes. The candidate genes were analysed for GO and KEGG pathway enrichment, and the significantly enriched pathways were condensed and classified to locate the biological processes affecting high and low lactation in Kazakh horses; the pathway enrichment chordal maps were drawn to further identify the genes related to lactation in Kazakh horses. 【Results】 GO and KEGG enrichment analyses found the largest number in cell development, proliferation, differentiation, adhesion-related and CNS and endocrine system developmental enrichment pathways, and the pathways of cell adhesion molecule binding, morphogenesis of differentiated cells, morphogenesis of cellular components, cellular development, PI3K-Akt signalling pathway, Axon guidance, and ECM receptor interactions affecting lactation. 【Conclusion】 It is determined that KIT, EPHA4, PDGFRA, MYH3, ITGA1, and COL4A1 may be candidate genes affecting lactation in Kazakh horses.