The telomere is a DNA/protein structure required to maintain the ends of linear chromosomes. Usually the DNA component comprises a highly conserved tandemly repeated minisatellite sequence. In most plants the minisatellite sequence is typically present in several hundred copies at each chromosome end, and is extended primarily by telomerase, which adds telomere repeats to the 3’ end. In the plant genus Allium, which contains around 700 species, there is an absence of typical telomeric DNA repeats. It is of great interest to determine what sequence or sequences have replaced the ancestral repeats and how they are lengthened. A range of molecular cloning methods were used to isolate candidate telomere sequences from the genomes of two diverged species, Allium cernuum and Allium cepa. I analyse several putative telomere sequences, isolated in this work and by others, but no proven candidate sequence has emerged. Nevertheless, one of those sequences, 35S ribosomal DNA (rDNA) encoding 35S rRNA, proved to have a structure that is previously not described for plants. I show that some units have a Ty1/copia retrotransposon fragment in the intergenic spacer region. Sequence analysis indicates that there was a single insertion followed by amplification, probably involving homogenisation mechanisms. Furthermore, I show high levels of rDNA length heterogeneity and rDNA unit divergence both within species and across the genus, respectively.