The examination and statistical analysis of loricate choanoflagellate material collected from Greenland waters during the period 1988-1998 represents a de facto baseline study of heterotrophic nanoflagellates from the Atlantic Arctic Region. The geographic sites sampled are Disko Bay (West Greenland) and the high-arctic North-East Water (NEW) and North Water (NOW) polynya. The analyses encompass close to 50 taxa. Some of these are described as new species, i.e. Acanthocorbis glacialis, A. reticulata and Diaphanoeca dilatanda. Two distinct clusters of species that are separated in time and space occur at all three sampling sites. A PCA analysis of NEW and NOW data points to that one community is linked to e.g. an early season high nutrient and low phytoplankton biomass scenario, whereas the other is predominant when nutrient levels are exhausted and the phytoplankton biomass high or declining. The material additionally allows for a comprehensive examination of e.g. the Cosmoeca ventricosa morphological variability encountered, as well as puts on record bimodal size variability within a number of species.