The Gram-positive, rod-shaped endophytic bacterium Cellulomonas sp. strain ATA003 was isolated from the endemic cactus Maihueniopsis domeykoensis seeds collected in the Coastal Atacama Desert, Chile. Here, we present a circular genome with a size of 4,084,881 bp and a GC content of 73.8% obtained by Nanopore sequencing. C1 [Bartholomaeus, Alexander; Mitzscherling, Julia; Lipus, Daniel; Wagner, Dirk] GFZ German Res Ctr Geosci, Sect Geomicrobiol, Potsdam, Germany. [Wagner, Dirk] Univ Potsdam, Inst Geosci, Potsdam, Germany. [Lavin, Paris] Univ Antofagasta, Fac Ciencias Mar & Recursos Biol, Dept Biotecnol, Antofagasta, Chile. [Contreras, Roberto; Oses, Romulo] Univ Atacama, Ctr Reg Invest & Desarrollo Sustentable Atacama CR, Copiapo, Chile. C3 Helmholtz Association; Helmholtz-Center Potsdam GFZ German Research Center for Geosciences; University of Potsdam; Universidad de Antofagasta; Universidad de Atacama