Two rapid, independent molecular assays have been developed for discriminating between the closely related rusts of hard pines, Cronartium flaccidum and Peridermium pini. A portion of the ITS region and a portion of the IGS region from the ribosomal RNA operon of the two organisms were amplified with the PCR. Amplifications were made using DNA extracted from aeciospores collected from unopened aecia, taking a small number of spores as a source of template DNA. Amplified fragments were subjected to RFLP or to SSCP analysis. Digests of the amplified products from the IGS1 region were electrophoresed on polyacrylamide gel and stained with ethidium bromide. Hinf I digestion of these fragments created polymorphic restriction profiles which allowed differentiation of the autoecious P. pini from the heteroecious C. flaccidum. Similar-sized DNA fragments representing the ITS2 region of the two rusts were denatured, subjected to electrophoresis as single strands on polyacrylamide gel under non-denaturing conditions and ‘silver stained’. The different mobility displayed by these short fragments revealed sequence polymorphism in the examined portion of the ITS region. This technique therefore represents an accurate and sensitive method for detection of base changes in given sequences of genomic DNA. A high level of homology was found between the two biotroph organisms in the loci screened. Results obtained in this trial indicate that PCR-RFLP and PCR-SSCP can be used as simple, speedy taxonomic tools for elucidating relationships among related organisms.