Telomere length is regulated by a complex interplay of several factors, including telomerase, telomere-binding proteins, DNA replication machinery and recombination. In yeast, DNA polymerase alpha is required for de novo synthesis of telomeres from broken ends of DNA, and it also suppresses the elongation of normal telomeric repeats. Heterochromatin proteins Clr1-Clr4 and Swi6 and DNA polalpha organize heterochromatin structure at mating type, centromere, rDNA and telomere regions that are refractory to transcription and recombination in Schizosaccharomyces pombe. Here, we have addressed the role of heterochromatin structure in regulating the integrity and organization of telomeric regions. Here, we show that subtelomeric duplication and rearrangements occur in polalpha and heterochromatin mutants and find that some of the putative duplication events are dependent on the Rad50 pathway. Thus, our study shows a role of heterochromatin in maintaining the integrity of the subtelomeric regions by suppressing their recombination in Sz. pombe.