Objective To evaluate the genetic diversity of ApoE gene in Z: ZCLA gerbil closed colony. Methods PCR-SSCP technique was employed to calculate the gene frequency, genotype frequency, heterozygosity, polymorphism information content of three SNPs of ApoE gene, which were reported in our previous work, in a total of 444 ordinary and clean Mongolian gerbils. Results The average allele of 3 SNP site 97, 981 and 1774 was 2. The inheritance pattern was in accordance with Mendel's law. Expected heterozygosities were 0.063, 0.501, and 0.499, and the average expected heterozygosity of whole group was 0.354. PIC were 0.061, 0375, and 0.374, with an average PIC of 0.270. Conclusion The ApoE gene frequency and genotype distribution in Mongolian gerbils may be to a certain degree associated with the genetic drift caused by long-term closed and selected breeding.