Spermatogenesis is the process of sperm cell formation; these cells constitute what an organism will contribute to the next generation, making their proper development essential for the preservation and continuity of a species. Among the different stages of spermatogenesis, meiosis is one of the most critical. Meiosis is a cell division process that involves a round of DNA replication followed by two consecutive divisions (meiosis I and II), ultimately producing haploid cells. During prophase of the first meiotic division, two crucial events take place: the pairing and recombination of homologous chromosomes. Pairing is essential for maintaining the species chromosome number, while recombination represents a fundamental source of biodiversity in sexually reproducing organisms. Both processes are mediated, at least in part, by a protein structure unique to meiosis: the synaptonemal complex (SC). In mammals, eight proteins have been identified as constituents of SCs. However, the molecular mechanisms enabling SCs to mediate the recognition, pairing, and recombination of homologous chromosomes remain unknown, as does the potential involvement of specific DNA sequences in this process, and more so, their identity. It has been shown that certain structural SC proteins, such as SYCP3 and SYCP1, are capable of binding DNA, although the specific bound sequences remain unidentified. In the present study, we aimed to evaluate the existence of specific SC-interacting nucleic acid sequences and determine their identity, using chromatin immunoprecipitation (ChIP) with anti-SYCP1 and SYCP3 antibodies, followed by library preparation and high-throughput sequencing of the DNA bound to these proteins (ChIP-seq). Bioinformatic analyses showed an enrichment in repetitive sequences, particularly those of the L1 type (for LINE-1, Long Interspersed Nuclear Element-1), followed by repeats of the ERVK class (Endogenous Retrovirus-K), a type of endogenous retrovirus. The association of SC components with this category of repeats has not been previously reported and may suggest a novel functionality for these sequences, which have often been regarded as “junk DNA”. Although these findings are still preliminary, the characterization of the identified sequences will contribute to the elucidation of the molecular bases underlying the interaction between the SC and chromatin, as well as their associated processes, which, despite their essentiality for all sexually reproducing organisms, are still poorly understood so far.