Fluorescence in-situ hybridization (FISH) of total genomic and repetitive DNA on microsporocytes of ditelocentric addition lines of rye 5RL in hexaploid wheat was performed to study the behaviour of the rye homologous chromosome arms in relation to centromere and telomere dynamics at premeiotic interphase and meiotic prophase I. By comparing isogenic lines with and without the Ph1 locus, we established the effect of the Ph1 gene on appearance and behaviour of the rye chromosomes. Ph1 and ph1b lines demonstrated similar premeiotic chromosome arrangement with the two rye homologues occupying separated domains despite the occurrence of centromere association. Our study confirmed that bouquet arrangement of telomeres follows the Rabl configuration. In cells displaying bouquet clustering of telomeres, centromeres of the 5RL telosomes are still at the opposite pole, suggesting anchoring of centromeres at the cytoskeleton. Once the telomeres complete clustering, the rye centromeres migrate to the telomere pole, and the rye chromosomes begin to loosen their structure. While the rye homologues in the wild-type keep separate territories in the nucleus, they become intermingled in the ph1b mutant, possibly because of their lower condensation. In a subsequent stage, the 5RL homologues appear intimately associated mainly at the distal region. Our study suggests that the lower rate of chromosome synapsis in the ph1b mutant results from abnormal chromatin decondensation and organization.