The Atmosphere Flagship programme addresses various topics, including analyses of long term meteorological observations, the interaction between the surface and the atmospheric boundary layer, the composition of the atmosphere with respect to climate active trace substances like aerosols or green house gases, as well as pollutants, the role of clouds in the Arctic atmosphere, interactions of the atmosphere with the snow covered ground, land-fast and drifting sea ice, surface UV spectral fluxes and its dependency on specific conditions in the stratosphere (ozone) as well as troposphere (clouds). Recently, the role of biogenic aerosols and the observation of black carbon in snow and atmosphere received particular attention. Within the Ny-Aalesund Atmosphere Flagship, we particularly highlight the connections to observations at Barentsburg, Pyramiden, and Hornsund, as well as the pan Svalbard meteorological network.