Recent national and international conservation legislation has led to an increased focus on ‘prioritised species lists’ for the allocation of conservation resources. However, prioritised species lists become problematic when there are difficulties in species delimitation.  One particularly complex group accounting for the majority of these problems is Euphrasia. The goal of this thesis is to use molecular markers to evaluate taxon limits and evolutionary processes in British Euphrasia to clarify the most appropriate approach for conservation. The results show that the major reproductive barrier in the group corresponds to ploidy level, with AFLP and chloroplast data both significantly differentiated between diploid and tetraploid species, although occasional gene flow via inter-ploidal hybridisation appears to contribute towards diversification of the diploid group. The genetic data support the current species level taxonomy for the diploid but not the tetraploid species, where a considerable overlap between taxa was detected. The chloroplast data detected four discrete lineages, the distribution of these among species suggest at least three allopolyploid events in the formation of the tetraploid taxa, within which distinct ecological groups occur. Variation in the breeding system was detected at the intra- and inter-specific levels and estimates of the inbreeding coefficient showed a strong correlation with flower size and support the importance of multiple shifts in breeding system as contributing towards the overall diversification within the group. Given the lack of clear species limits in the tetraploid group and the dynamic nature of Euphrasia evolution, a change from a species- to process-based conservation approach is recommended. This charge include recognising the importance of progenitor taxa, and ecological and morphological diversity, and a decrease in the importance presently given to individual named endemic taxa.