Objective DNA methylation microhaplotype (DMH) refers to the combination of multiple methylation sites in a very short range, and its haplotypes are rich in diversity. Screening and validation of age-related DNA methylation microhaplotypes in mouse blood. Methods First, a theoretical dataset of DNA methylation microhaplotypes based on the mouse reference genome was constructed. Second, age-related DNA methylation microhaplotypes were screened by Spearman's rank correlation analysis using high-throughput sequencing information of DNA methylation in mouse blood from a network database. Finally, cross-validation was performed with a validation dataset. Results The number of DNA methylation microhaplotype sites within 50 bp in the mouse genome totaled 6,787,142, and DNA methylation microhaplotypes consisting of single-digit CpG sites accounted for 98.64 %. A total of 5,835 age-associated DNA methylation microhaplotypes were screened in 58 mouse blood samples (Spearman's rank correlation test, |rho| > 0.5, P < 0.01), and they accounted for 0.086 % of DNA methylation microhaplotypes. Finally, the top one hundred age-associated DNA methylation microhaplotypes with high correlation were validated in 95 independent samples, resulting in 44 loci. Conclusion The age-associated DNA methylation microhaplotypes screened in this study can be useful for future mouse blood apparent age prediction and aging studies.