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Abstract: Characterising how deep-sea communities change on contemporary time-scales and understanding underlying ecosystem processes has become important under changing climate and the rise in the exploitation of deep-sea resources. However, little is known about these dynamics and processes. Long-term observations from which inter-annual variations can be detected are scarce in the deep sea. This study examines inter-annual changes in density, family richness and evenness, family and functional group rank abundance distributions of infaunal polychaetes at two abyssal stations in the North East Pacific (Station M, 1991 to 2005) and in the North East Atlantic (Porcupine Abyssal Plain, 1991 to 1999). The two long-term data sets were used to investigate not only if polychaete community structure and composition varied at inter-annual scales in terms of diversity and rank abundance distributions but also if any changes were related to previous observations in megafauna and environmental factors at each locality. The polychaete community structure at each locality was analysed using univariate statistics as well as multivariate ordination techniques based on Bray-Curtis similarity of the yearly family density. Sub-surface deposit feeders, such as Paraonidae, dominated the North East Pacific, whereas surface deposit feeders, such as Cirratulidae, dominated the North East Atlantic. Both stations showed inter-annual variations in density, family evenness and rank abundance distributions. The greatest changes occurred in 1998 in both time series when polychaete densities peaked, and switches in the rank abundance of the most abundant families and functional groups took place. Inter-annual variations in the polychaete community were correlated with a limited number of holothurian species changes, but no correlation was found with particulate organic matter flux or climate indices. Ecological and environmental factors behind the family-level changes remain elusive. Overall, changes in the dominance of functional groups imply changes in abyssal ecosystem functioning with potential consequences on carbon cycling at the seabed. [Copyright &y& Elsevier]