The male-specific region of Y chromosome (MSY) has accumulated a higher density of human endogenous retroviruses (HERVs) and related sequences when compared with other regions of the human genome. Here, we focused on one HERV family, HERV-K14C that seemed to integrate preferentially into the Y chromosome in humans. To identify every copies of HERV-K14C in the human genome, we applied computational screening to map precisely the locus of individual HERV-K14C copies. Interestingly, 29 of all 146 copies were located in Y chromosome, and these 29 copies were mostly dispersed in the palindromic region. Three distinct HERV-K14C-related transcripts were found and were exclusively expressed in human testis tissue. Based on our phylogenetic analysis of the solitary LTRs derived from HERV-K14C on the Y chromosome we suggested that these sequences were generated as pairs of identical sequences. Specifically, analysis of HERV-K14C-related sequences in the palindromic region demonstrated that the Y chromosomal amplicons existed in our common ancestors and the duplicated pairs arose after divergence of great apes approximately 8-10 million years ago. Taken together, our observation suggested that HERV-K14C-related sequences contributed to genomic diversification of Y chromosome during speciation of great ape lineage.