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Mitochondrial DNA (mtDNA) replication is orchestrated by nuclear‐encoded proteins but occurs independently of nuclear DNA (nDNA) replication. It has been previously shown that cell‐cycle arrest induces excessive accumulation of mtDNA molecules in Saccharomyces cerevisiae cells. On the one hand, mtDNA overreplication decreases yeast viability during prolonged (more than 10 hours) cell cycle arrest in S‐phase. On the other hand, yeast cells can survive extremely long cell‐cycle arrest in G1‐phase induced by destabilization of SCF ubiquitin‐protein ligase complex cdc34. Thus, we suggested that there are mechanisms limiting mtDNA replication under prolonged cell cycled arrest. We also suggested that Rho‐ mitochondrial DNA with large deletions can avoid such control mechanisms. To test these suggestions we studied the accumulation of the wild type (Rho+) and the mutant (Rho‐) mtDNAs in yeast cell arrested in different phases of the cell cycle. We used yeast strains with thermosensitive mutations in the genes that induce arrest in different stages under the restrictive temperatures: cdc13‐1 (S/G2), cdc15‐2 (telophase), Δcdc26 (metaphase), cdc34‐2 and cdc53‐1 (G1/S). MtDNA/nDNA ratios were estimated using qPCR. Additionally, total DNA content was analyzed by measuring the fluorescence of the DNA‐intercalating agent propidium iodide (PI) using flow cytometry. Surprisingly, we did not observe a significant increase in the mtDNA/nDNA ratio in the arrested cells regardless of their mtDNA genotype after 9 h or 24 h of cell cycle arrest in any stage by the qPCR analysis (n=4‐6). However, we did observe an increase in the total fluorescence of PI in the arrested cells that indicated an accumulation of DNA molecules different from those that are detected by qPCR. We propose that these fragments can be abortive mtDNA replication products or rDNAs. Together, our data suggest that there are mechanisms limiting excessive mtDNA accumulation during prolonged cell cycle arrest in yeast. Deletion of large fragments in mtDNA does not allow to evade these mechanisms. The work was supported by RFBR grant 19‐04‐00782.