Measurement of metabolic rates (made at 10A degrees C) of individuals of the springtail Cryptopygus antarcticus travei from six geographically distinct populations on sub-Antarctic Marion Island were combined with mitochondrial DNA (COI) haplotype analysis to examine in parallel both physiological and genetic variation of distinct populations. We found evidence of genetic differentiation among populations and a general indication of long-term isolation with limited gene flow. While we found support for an overall pattern of metabolic rate structure among populations from different geographic locations on the island (mean rate = 0.0009-0.0029 mu l O(2) mu g(-1) h(-1) for populations of a mean individual mass of 8-26 mu g), we were unable to demonstrate a coherent common pattern between this and genetic variation. However, spatial structure in metabolic rate variation was strongly related to the extent of variability in microclimate among sites, and also showed some indication of a phylogeographic signal. Thus, over the relatively short timescale of Marion Island s history (<1 million years), the periodic geographic barriers that have driven population differentiation from a molecular perspective may also have resulted in some physiological differentiation of populations.