We studied sequence variation of a fragment of the mitochondrial cytochrome b gene using polymerase chain reaction (PCR) and direct sequencing of 109 Atlantic cod (Gadus morhua) from the Baltic and 19 cod from the White Sea. Eight nucleotide substitutions define 12 haplotypes differing from each other by one to six substitutions. All mutations are at silent sites and thus neutral to selection arising from protein action. Frequencies of four common haplotypes are 6%–57% and haplotype diversity is 0.64 ± 0.031. Testing for neutral theory predictions reveals no departure from neutrality. The Baltic shares its haplotypes with distant localities in the Atlantic but differs in frequency. Within the Baltic none of the variation is explained by geographic location with an AMOVA. Temporal changes of haplotype frequencies of up to 50% are observed between sampling years and yearclasses. A potential confounding of temporal and microspatial variation cannot be excluded due to limited sample size.