Colobanthus quitensis (Caryophyllaceae) is one of only two vascular plants native to Antarctica and a model species for studying adaptation to extreme environments. We report a chromosome-scale reference genome generated from PacBio HiFi and Hi-C sequencing. The final assembly spans 887.1 Mb and resolves into 40 chromosome-scale scaffolds (2n = 80), with a scaffold N50 of 20.4 Mb and a maximum scaffold length of 35.1 Mb. Assembly completeness was high, with 99.0% of embryophyta BUSCOs recovered, the majority as duplicated (95.7%), consistent with the species’ putative tetraploid origin. The genome exhibits a GC content of 36.3%. We further assembled the complete chloroplast genome (151,314 bp; 113 genes) and a draft mitochondrial assembly comprising two partial contigs totaling ∼289 kb. Repeat annotation identified 69.9% of the genome as repetitive, with long terminal repeat retrotransposons as the dominant class (34.8%), primarily of the Ty1/Copia and Gypsy/DIRS1 superfamilies. A total of 40,762 protein-coding genes were predicted, of which 95% were functionally annotated. Combined with transcriptomic resources, this genome enables functional annotation and comparative studies. This is the first chromosome-scale assembly for an Antarctic angiosperm and a resource for investigating polyploidy, genome organization, and adaptive evolution in polar environments. The C. quitensis genome will also support ecological and applied studies, including the development of crops resilient to cold and other abiotic stresses.