In order to estimate the nucleotide diversity of the four kelp species Laminaria digitata, L. hyperborea, L. saccharina and L. faeroensis, three approaches were used. First we sequenced 1320 base pairs (bp) of nuclear-encoded large subunit (LSU) rDNA, which included some of the most variable domains. These sequences discriminated between L. digitata, L. hyperborea and L. saccharina, but L. faeroensis was identical to L. saccharina. A phylogeny inferred based on 672 bp of the nuclearencoded non-coding internal transcribed spacer regions (ITS1 and ITS2) rDNA, which are more variable than LSU rDNA, likewise failed to resolve a monophyletic L. saccharina with respect to L. faeroensis. Thirdly, we tested the usefulness of the amplified fragment length polymorphism (AFLP) technique to provide a resolved phylogeny for 43 Laminaria specimens. Laminaria digitata and L. hyperborea were resolved as strongly supported monophyletic groups. A third robust clade consisted of L. saccharina plus L. faeroensis. Within this clade, L. faeroensis samples were grouped with bootstrap support of 80%, but the L. saccharina clade was less well supported. The AFLP data in combination with rDNA sequences indicated subspecies status for L. faeroensis. AFLP analyses of different morphotypes of L. digitata and L. saccharina from Danish coastal waters did not reveal any differences. However, L. digitata from the Faroe Islands was genetically distinct from other samples.