The genus Cochlearia is a taxonomically complex genus with a circumpolar distribution. In common with many other post-glacial colonisers it exhibits complex patterns of morphological and ecological variation. The genus has been the subject of continued taxonomic controversy, especially within the species complex C. officinalis s.l. The focus of this study was to investigate whether the three rare putative endemic Cochlearia officinalis s.l. taxa in Britain: C. micacea, C. officinalis subsp. scotica and C. atlantica were sufficiently distinctive to warrant endemic species or taxon status at any rank. Furthermore, to make conservation recommendations for the species complex based on the outcome of this investigation. The patterns of differentiation in Cochlearia were studied to gain insight into the processes that have driven morphological and ecological diversification in the group. The six putative taxa in Cochlearia officinalis s.l. were considered in this study: C. officinalis s.s., C. officinalis subsp. scotica, C. pyrenaica subsp. pyrenaica, C. pyrenaica subsp. alpina, C. atlantica and C. micacea. Samples of C. danica, a member of the wider genus Cochlearia, were also included for comparison. The samples were screened for variation in AFLP fragments, morphological characters and chloroplast haplotypes. This is the first study focussed on the British Cochlearia to use the amplified fragment length polymorphism (AFLP) technique. Many qualitative morphological characters differences between populations were maintained in cultivation under standard conditions. Variation in some quantitative morphological characters was significantly different between taxon groups. The morphological characters combined did not distinguish between taxonomic groups. Variation was found in samples from the uplands only. Although there were three chloroplast haplotypes all but 6 out of 96 samples had the same haplotype and the chloroplast was not taxonomically informative. The AFLP data did not vary significantly between taxonomic groups, ploidy levels, habitats or geographical regions. There was significant AFLP variation between populations. The morphological and ecological diversity present among populations of Cochlearia officinalis s.l. in Britain is most likely to result from local ecotypic differentiation. The variation in Cochlearia officinalis s.l. could not be divided satisfactorily into taxa of species rank and so specific conservation of taxa within the complex is not recommended. Instead the maintenance of Cochlearia diversity can be achieved by the continued protection of the habitats in which the ecotypes grow.