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<i>Stevia rebaudiana</i> is one of the most important crops belonging to the Asteraceae family. Stevia is cultivated all over the world as it represents a valid natural alternative to artificial sweeteners thanks to its leaves, which produce steviol glycosides that have high sweetening power and reduced caloric value. In this work, the stevia genome sequence was used to isolate and characterise full-length long-terminal repeat retrotransposons (LTR-REs), which account for more than half of the genome. The <i>Gypsy</i> retrotransposons were twice as abundant as the <i>Copia</i> ones. A disproportionate abundance of elements belonging to the <i>Chromovirus/Tekay</i> lineage was observed among the <i>Gypsy</i> elements. Only the <i>SIRE</i> and <i>Angela</i> lineages represented significant portions of the genome among the <i>Copia</i> elements. The dynamics with which LTR-REs colonised the stevia genome were also estimated; all isolated full-length elements turned out to be relatively young, with a proliferation peak around 1–2 million years ago. However, a different analysis conducted by comparing sequences encoding retrotranscriptase showed the occurrence of an older period in which there was a lot of LTR-RE proliferation. Finally, a group of isolated full-length elements belonging to the lineage <i>Angela</i> was used to analyse the genetic variability in 25 accessions of <i>S. rebaudiana</i> using the Inter-Retrotransposon Amplified Polymorphism (IRAP) protocol. The obtained fingerprints highlighted a high degree of genetic variability and were used to study the genomic structures of the different accessions. It was hypothesised that there are four ancestral subpopulations at the root of the analysed accessions, which all turned out to be admixed. Overall, these data may be useful for genome sequence annotations and for evaluating genetic variability in this species, which may be useful in stevia breeding.