An electrophoretic survey of 81 populations of arctic Daphnia pulex from around the Svalbard archipelago revealed the presence of 49 unique allozyme clones (N = 3357). Two closely related clones accounted for 66% of the total sample, and were widespread across the archipelago. Restriction fragment length polymorphisms (RFLPs) of a 2.1-kb fragment of mtDNA (NADH-4 and NADH-5 subunits), amplified using the polymerase chain reaction (PCR), revealed the presence of eight mtDNA haplotypes. One haplotype was particularly widespread, and the two most abundant allozyme clones shared this haplotype. Nonrandom distribution patterns of clones were observed, and are most likely the result of historical events (i.e. founder effects) related to the past glacial history of the archipelago. The data are discussed with reference to past glaciation events, and attempts are made to discern the colonization history of this apomictic complex.