Neltuma alba (Algarrobo blanco), Neltuma chilensis (Algarrobo Chileno) and Strombocarpa strombulifera (Fortuna) are some of the few drought resistant trees and shrubs found in small highly fragmented populations, throughout the Atacama Desert. We reconstructed their plastid genomes using de novo assembly of paired-end reads from total genomic DNA. We found that the complete plastid genomes of N. alba and N. chilensis are larger in size compared to species of the Strombocarpa genus. The Strombocarpa species presented slightly more GC content than the Neltuma species. Therefore, we assume that Strombocarpa species have been exposed to stronger natural selection than Neltuma species. We observed high variation values in the number of cpSSRs (chloroplast simple sequence repeats) and repeated elements among Neltuma and Strombocarpa species. The p-distance results showed a low evolutionary divergence within the genus Neltuma, whereas a high evolutionary divergence was observed between Strombocarpa species. The molecular divergence time found in Neltuma and Strombocarpa show that these genera diverged in the late Oligocene. With this study we provide valuable information about tree species that provide important ecosystem services in hostile environments which can be used to determine these species in the geographically isolated communities, and keep the highly fragmented populations genetically healthy. C1 [Contreras-Diaz, Roberto] Univ Atacama, Ctr Reg Invest Desarrollo Sustentable Atacama CRID, Copayapu 485, Copiapo, Chile. [Carevic, Felipe S.] Univ Arturo Prat, Fac Recursos Nat Renovables, Lab Ecol Vegetal, Campus Huayqu, Iquique, Chile. [Contreras-Diaz, Roberto; Carevic, Felipe S.] Nucleo Milenio Ecol Histor Aplicada Bosques Aridos, Santiago, Chile. [van den Brink, Liesbeth] Univ Concepcion, Fac Ciencias Nat & Oceanograf, Dept Bot, ECOBIOSIS, Concepcion, Chile. [Huanca-Mamani, Wilson] Univ Tarapaca, Fac Ciencias Agron, Ctr Genet & Genom UASARA, Lab Biol Mol Plantas, Arica 1000000, Chile. [Jung, Patrick] Univ Appl Sci Kaiserslautern, Integrat Biotechnol, Carl Schurz Str 10-16, D-66953 Pirmasens, Germany. C3 Universidad de Atacama; Universidad Arturo Prat; Universidad de Concepcion; Universidad de Tarapaca; University of Kaiserslautern