This paper undertakes an exploration of the potential application of the Weitzman prioritisation approach to the conservation of plant genetic resources (PGR). Using a case study approach and assuming limited conservation resources, this approach is applied to calculate the maximum diversity which can be conserved based on a clustering of cacao species (Theobroma cacao L.). A conservation budget allocation model applied across a set of ten clusters and nine subclusters of cacao, together with the use of alternative diversity and risk measures, allowed for an evaluation of a range of potential conservation outcomes. Alternative risk measures generally resulted in the allocation of conservation funds to the same priority clusters of cacao (Criollo and Curaray). However, the use of the number of locally common alleles as an alternative to the original Weitzman diversity measure produced a markedly different result, prioritising the Purús cluster in Western Amazonia. The Curaray cluster was highly prioritised under both diversity measures, indicating its distinctiveness relative to both the Criollo and Purús clusters. We conclude that the Weitzman approach can indeed allow diversity comparisons to be made between the outcomes of different PGR conservation strategies, although subjective decisions regarding the choice of diversity and risk measures remain.