Here we hypothesise that interspecies geneflow as well as secondary contact of formerly isolated clusters of T. landbeckii may have contributed to maintain, restore or even enhance the species´ genetic diversity through space and time. We employed genotyping-by sequencing (GBS) to obtain genetic variation largely retrieved from the nuclear genome on population level, and used the same data to extract sequence information to define maternally inherited plastid types. Reference plastomes from different plastid types via a genome-wide short read sequencing approach (genome skimming) were assembled. Plastome data were analysed in order to provide a robust phylogenetic and temporal framework of the maternal perspective including various epiarenic species of particular interest for the evolutionary history of T. landbeckii. The spatiotemporal scale of our study covers the entire Chilean Atacama Desert with a focus on one population form the central cluster. The aim of our study is to provide reasonable explanations for orphan genetic clusters on different spatial scales, while highlighting the idea of evolutionary significant secondary genetic contact on and between species level, which may have also fostered the evolution of epiarenic growth in Tillandsia. This study should pave the way for future comparative evolutionary studies across epiarenic Tillandsia species to unravel the co-evolution of the Atacama Desert system and biological life.