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Abstract Aim To determine patterns in diversity of a major Antarctic plant species, including relationships of Antarctic populations with those outside the Antarctic zone. Location Antarctic Peninsula, Maritime Antarctica, sub-Antarctic islands, Falkland Islands and South America. Methods Amplified fragment length polymorphisms (AFLPs) and chloroplast sequences were used to study patterns of genetic diversity in Antarctic hairgrass (Deschampsia antarctica Desv.) and the genetic relationships between populations over its distribution range. Thirty-eight populations were sampled from a large part of the distribution of D. antarctica, and additionally, herbarium specimens were included for areas from which we could not obtain fresh samples. Results A gradient in AFLP diversity was observed going from the Falklands southwards into the Antarctic. This gradient in diversity was also observed within the Antarctic Peninsula: diversity was lower further south. Diversity in the chloroplast genome of D. antarctica was low. Only three chloroplast haplotypes were found, each with a strong regional distribution. Main conclusions The phylogenetic construction of AFLP marker frequencies in meta-populations of D. antarctica supports a stepping-stone model of colonization, whereby gene flow mainly occurs between neighbouring populations. It is concluded that long-distance gene flow is very limited in D. antarctica. A very low diversity was found in the sub-Antarctic islands in the Indian Ocean, indicating that these populations have experienced a recent evolutionary bottleneck.