White whales are found all around Svalbard, but their population structure in this area is unknown. A recent study using telemetry showed that the animals tagged in the Van Keulen/Van Mijenfjorden and Storfjorden in the southern parts of Svalbard only travelled in the southern areas of Svalbard. Because they never migrated to the northern parts of Svalbard this could indicate two or more separated sub-populations of white whales in the Svalbard waters. The aim of the present study was to analyze the population structure of the white whales around Svalbard by using molecular markers (the D-loop region of the mitochondrial DNA and seven microsatellite loci). This was done by comparing individual whales mainly from Krossfjorden in the northwestern part of Svalbard with individuals from Storfjorden in the southeastern parts of Svalbard to see if there are significant differences in the allele frequencies and haplotypes from these two regions. An analysis of molecular variance (AMOVA) based on the mitochondrial haplotypes showed a higher variation within the sample areas (96.79 %) than between the sample areas (3.21 %). The program STRUCTURE did not detect any structuring of the samples based on the seven microsatellite loci, and found just one cluster of individuals (K=1) most likely. A significant differentiation (FST) between the two sample locations was found for both the mitochondrial haplotypes (FST = 0.119, P < 0.0001) and the microsatellite loci (FST = 0.01551, P = 0.01802 +/- 0.0121), but due to the small sample size, matrilineal pod structure and other deviations from the underlying assumptions this was only used as descriptors. A minimum spanning tree indicated some clustering of the mitochondrial haplotypes but these clustering did not correspond to the sample locations. A gender segregation of habitat use was found, as the Krossfjorden area was used mainly by all male groups. From the current results it seems that the studied part of Svalbard only contains one population. However, further analyses with more samples covering more areas of Svalbard and more loci are advised. Also the gene-flow and possible mixing of whales with the Karskaya population in the western Russian Arctic should be addressed.