Caging experiments were performed at the Arctic deep-sea long-term observatory HAUSGARTEN to investigate the effects of megafauna exclusion on nematode assemblages. Six experimental cages were deployed at 2500 m water depth and sampled after 4 years for meiofauna and a series of sediment parameters. With the exception of chlorophyll a and phaeopigments, which were significantly higher inside the cages, sediment parameters did not differ between inside and outside the cages. Yet multivariate analysis of the sedimentary environment showed a higher variability outside the cages, indicating higher environmental heterogeneity in the presence of megafauna. Nematode densities (aver. 1516 ind 10 cm-2) were significantly higher in sediments from inside the cages, whereas total number of species (aver. 70 sp.), Shannon-Wiener diversity (aver. 3.4) and Pielou evenness (aver. 0.8) did not differ between the two treatments. Also differences in faunal multivariate structure between cage and control samples were not significant. Nevertheless, Fisher's alpha diversity, the number of nematode genera and taxonomic distinctness showed significantly higher values outside the cages. Since univariate measures are often insensitive to changes in community structure, and interpretation of the multivariate analysis was confounded by the large number of rare species, we further analysed our data by dividing the species into three groups of frequency (frequent, intermediate and occasional) and into three groups of abundance (dominant, sub-dominant and scarce). Results from this analysis revealed that the higher nematode abundances inside the cages were mainly due to an increase in density of scarce species that were either frequent or intermediate in frequency. In contrast, occasional species were adversely affected. These results lead us to believe that it is mainly the frequent species occurring in low densities that take advantage of favourable conditions (i.e. lack of disturbance or increased phytodetritus) in the deep sea. The higher taxonomic distinctness, Fisher's diversity, and number of genera at the control sites, together with the fact that they were environmentally more heterogeneous, suggest that megafaunal organisms play an important role in creating microhabitats in the sediment and significantly influence deep-sea nematode assemblages. However, the lack of any changes in species richness inside the cages after 4 years suggests that they cannot fully account for the maintenance of the remarkable high levels of species coexistence in the deep sea. The key is more likely to be found in evolutionary history than actual ecology. © 2007 Elsevier Ltd. All rights reserved.