Satellite dna s (satDNA) have long been recognized as a major driving force in karyotypic repatterning, owing to their ability to recombine between non-homologous chromosomes. A quite extensively studied model is the Repetitive PvuII Ctenomys Sequence (rpcs), the main component of constitutive heterochromatin in rodents of the genus Ctenomys (Rodentia, Ctenomyidae). At the genus level, fluctuations in rpcs copy number have been previously associated with karyotypic instability. However, when a microevolutionary approach was assayed in the most karyotypically variable lineage of the genus, the vast population-level copy number variation precluded any possibility of analyzing it in a phylogenetic framework. The existence of sex-related differences as a source of variability was not considered until later, when chromosomal banding suggested that the Y chromosome may be a significant reservoir of rpcs. This study aimed to investigate the bias associated with the presence of the Y chromosome in rpcs copy number variation in the Corrientes group of Ctenomys. The results revealed that the Y chromosome harbors almost twice the amount of rpcs compared to the rest of the chromosome complement, explaining the high levels of intrapopulation variation. The evolution of rpcs copy number in males and females showed independent patterns, attributable to the presence/absence of the Y chromosome. The correlation between rpcs dynamics and diploid number fluctuations was also investigated, concluding that some karyotypic repatterning events could be explained by satDNA amplification/deletion, but not all of them. This study highlights the importance of considering differences resulting from the differential accumulation of satDNA in the heterogametic chromosome.