Our data demonstrated an association between KRAB-ZFP-binding motifs and the DNA demethylation resistance of L1, SVA, and LTR12. ZNF649, ZNF257/28, and ZNF850 were associated with DNA demethylation resistance of L1, SVA, and LTR12C, respectively. The dynamics of DNA methylation during spermatogenesis are largely different among retroelement types. The majority of L1 copies acquired DNA methylation during spermatogenesis, whereas the DNA methylation status of LTR12 in human primordial germ cells (hPGCs) tended to be maintained during spermatogenesis. The mode of DNA methylation changes in SINE-VNTR-Alus (SVAs) during spermatogenesis largely differs between copies and individuals. SVA copies located in highly transcriptionally active regions acquire DNA methylation during spermatogenesis, while those located in transcriptionally inactive regions maintain a hypomethylated state during spermatogenesis. In contrast, the degree of DNA methylation in sperm in SVA copies located in low transcriptionally active regions was highly variable among the individuals. These results suggest that SVAs may be methylated by transcription-directed DNA methylation mechanisms during spermatogenesis, and their activity varies among individuals.