Background <p>The subtelomeric region of the 1RS arm of rye (<i>Secale cereale</i> L.) contains several kinds of tandem repeats with high copy number and they can affect meiotic recognition and pairing of this chromosome arm. However, whether different tandem repeats exert distinct effects on meiotic behavior remains unclear.</p> Results <p>Four types of F₁ plants (Group1-Group4) were generated using nine wheat-rye 1BL.1RS translocation cultivars/lines in which the copy number of tandem repeats pSc200 and pSc250 on 1RS changed. The pSc200 disappeared from one of the 1RS in Group 1 and its copy number was different between the two 1RS arms in Group 2. The copy number of pSc250 was different in Group 3. No visible difference on pSc200 or pSc250 can be discerned with naked eye between the 1RS arms in Group 4. The frequencies of bouquet association, pachytene pairing and chiasmata of 1RS were all significantly higher in Group 2 than that in Group 1. No great difference in 1RS pairing frequency existed among Groups 2, 3 and 4. However, the chiasmata frequency in Group 2 was significantly lower than that in Group 3 and Group 4. It seems that the effect of pSc200 on the meiotic behavior of 1RS was greater than that of pSc250, and the copy number of pSc200 could affect the pachytene pairing and crossover of 1RS. Both 1RS in Group 3 and Group 4 displayed normal meiotic behavior. These might be used to explain how the subtelomeric regions of homologues affect their meiotic behavior.</p> Conclusions <p>The influence of tandem repeat pSc200 on meiotic pairing and chiasmata of 1RS was greater than that of tandem repeat pSc250. Reducing the difference in pSc200 copy number between the two 1RS arms would enhance the frequencies of their bouquet association, pachytene pairing and crossover.</p>