We are interested in developing a method for the identification of those genes in malaria parasites which underlie a variety of selectable phenotypes of the parasites including drug resistance and strain-specific immunity. A key aspect of our approach is to subject a genetically mixed population of malaria parasites to a specific phenotypic selection pressure such as the administration of an antimalarial drug and then identify genetic markers affected by the selection. Our aim, therefore, is to be able to identify those genetic markers carried by sensitive parasites which disappear from the population after selection as they should be closely linked to the locus determining the phenotype involved. We have previously identified more than 800 amplified fragment length polymorphisms (AFLP) distinguishing two cloned strains of the rodent malaria parasite Plasmodium chabaudi chabaudi and distributed across the whole of the parasites' genome. Here we evaluate the possibility that the intensities of these AFLP bands are quantitatively related to the proportions of parasite DNA which bear these markers in mixtures of genetically different parasites. We prepared mixtures of DNA and parasitised blood from different mixtures of two genetically distinct clones (AS and AJ) of P. c. chabaudi and analysed AFLP markers amplified from them. The results show that the relative band intensities of AFLP markers are, indeed, linearly related to the proportions of parasite DNA in a genetically mixed sample. The precision of the method is sufficient to detect reliably the effects of phenotypic selection at loci closely linked to a genetic locus under selection.