The Curonian Spit (Lithuanian: Kursiu nerija) is a 98 km long, thin, curved sand-dune spit that separates the Curonian Lagoon from the Baltic Sea coast. The Curonian Spit is home to the highest moving (drifting) sand dunes in Europe. Coniferous woods are prevalent in the Kursiu Nerija National Park (80%). These woods consist mostly of native Scots pine (Pinus sylvestris L.) and alien mountain pine (Pinus mugo L.). With the planting of non-native species, there is a need for studies evaluating the effects of alien and native plant species on soil ecosystem properties. We measured soil microbial communities from nearby pairs of native and alien pine species. Forty-two sampling sites of close-growing P. sylvestris and P. mugo were selected. To measure the soil microbial activity in these sites, we used Biolog EcoPlates. We found that the functional diversity of microorganisms that use carbon sources was significantly greater in the mature pine stands. Microbial functional diversity was also greater in the soils of native pine stands. Differences between activity and functional diversity in newly established and old stands were also identified.