There are different views on the underlying causes of the suggested genetic differentiation of cod groups in some regions of its distribution (e.g. Norway and Iceland). These are the historical (historical genetic isolation of groups) and selection (high genetic differentiation at selected loci) hypotheses.  The first corresponds to a scenario of historical genetic isolation of groups, while the latter describes a scenario of high genetic differentiation at selected loci.  The first indicates a scenario of historical genetic isolation of groups and the latter a scenario of high genetic differentiation at selected loci. The pantophysin (Pan I) locus, acknowledged to be under selection, indicates high population differentiation in contrast with other, presumably neutral, loci.  The Pan I gene has two alleles, Pan I^A and Pan I^B corresponding to absence or presence of a Dra I restriction site, which are highly divergent at nucleotide and amino acid level. Here we test the predictions of a historical hypothesis of population division in Iceland, namely non-random distribution %of individuals in gene genealogies of polymorphisms segregating within each major allele, i.e. that individuals from the same clade would belong to the same geographic region or the same depth class.