Phylogenetic divergence in Asparagales plants is associated with switches in telomere sequences. The last switch occurred with divergence of the genusAllium(Amaryllidaceae) from the other Allioideae (formerly Alliaceae) genera, resulting in uncharacterized telomeres maintained by an unknown mechanism. To characterize the unknownAlliumtelomeres, we applied a combination of bioinformatic processing of transcriptomic and genomic data with standard approaches in telomere biology such as BAL31 sensitivity tests, terminal restriction fragment analysis, the telomere repeat amplification protocol (TRAP), and fluorescencein situhybridization (FISH). Using these methods, we characterize the unusual telomeric sequence (CTCGGTTATGGG)n present inAlliumspecies, demonstrate its synthesis by telomerase, and characterize the telomerase reverse transcriptase (TERT) subunit ofAllium cepa. Our findings open up the possibility of studying the molecular details of the evolutionary genetic change inAlliumtelomeres and its possible role in speciation. Experimental studies addressing the implications of this change in terms of the interplay of telomere components may now be designed to shed more light on telomere functions and evolution in general.