Tillandsia landbeckii Phil. is a typical plant of the Atacama Desert in the north of Chile. There is no genetic data available at the population level for this species, and this information is critical for developing and implementing effective conservation measures. In this study, we investigated for the first time the genetic diversity and population structure in 2 natural populations of T. landbeckii using AFLP markers. Seven primer combinations produced 405 bands and of them, 188 (46.42%) were polymorphic. The Pampa Dos Cruces population (Pp = 88.30%, He = 0.327, and I = 0.483) showed a higher genetic diversity level than Pampa Camarones population (Pp = 71.28%, He = 0.253, and I = 0.380). Analysis of molecular variance (Amova) revealed that 25.12% of the total genetic diversity resided among populations, while 74.88% within populations. A moderate-high genetic differentiation coefficient (Fst = 0.251) and a moderate population gene flow (Nm = 1.490) were also observed. Principal coordinates analysis (PCoA), Neighbor-net and STRUCTURE analysis supported the grouping of the sampled populations into 2 moderate genetic clusters. This first study provides data that will allow assist and support conservation decisions taken for this species.