Populations of Antarctic hairgrass Deschampsia antarctica Desv. from King George Island exhibit variation in many traits. The reason for that is not evident and could be addressed to variable environmental conditions. Obviously, phenotypic variation could be due to stable or temporal changes in expression pattern as the result of adaptation. Stable changes could be due to mutations or site DNA methylation variation that modified expression pattern. Recently, metAFLP approach was proposed to study such effects. A variant of methylation sensitive AFLP (Amplified Fragment Length Polymorphism), based on the isoschizomeric combinations Acc65 I/ Mse I and Kpn I/ Mse I was applied to analyze the sequence and site DNA methylation differences between two D. antarctica populations exhibiting morphological dissimilarities. Both DNA sequence mutations and site methylation pattern alternations were detected among and within analyzed populations. It is assumed that such changes might have originated as the response to environmental conditions that induced site methylation alternations leading to phenotypic variation of D. antarctica populations from South Shetland Islands.