ABSTRACT: We used allozymes to investigate the population genetics of the sea star Coscinasterias muricata throughout New Zealand, with emphasis on populations inhabiting the fjords on the west coast of the South Island. Mean genetic variabilitymeasured by Wright¹s F_st for all the New Zealand populations was 0.061, indicating a moderate level of genetic divergence on a New Zealand wide scale. F_st for populations from the fjord region was generally lower,ranging from 0.024 to 0.028, but it deviated from zero for all the loci examined. Evidence of isolation by distance was found when all populations were used in an analysis of log of the extent of gene flow between a pair of populations (M–) againstthe log of geographic distance (r² = 0.57, p < 0.001, Mantel test). Thus, a pattern of isolation by distance seems evident on this larger scale. However, pair-wise comparisons of genetic distances, measured as F_st ,of populations on the regional scale of the fjords on the west coast of the South Island showed no correlation, since high variation of F_st (0.001 to 0.09) between populations separated by 20 to 105 km was detected. The overall patternof genetic variation revealed in a cluster analysis of genetic identity, I, grouped all the fjord populations together with maximum genetic identities of 94.6% to the other South Island populations, but within the fjord region, populations were notsegregated according to geographical location. We suggest that the relatively isolated hydrography of each fjord is a most likely explanation for why fjord populations form genetic clusters that are inconsistent with geographical distance. The NewZealand fjords changed from freshwater systems about 12000 to 6500 yr ago, and genetic equilibrium for the populations that colonized the fjords may not have been reached yet. We suggest that the recent colonization of the fjords, and the physicalisolation from the open coast and each other, are important in explaining the genetic pattern of fjord populations of C. muricata.