A set of 44 bread wheat landraces was used to determine the efficacy of 16-amplifed fragment length polymorphism (AFLP) primers and 63 wheat simple sequence repeat (SSR) markers in identifying polymorphisms between accessions. The SSR markers detected approximately 10 alleles per locus with a mean gene diversity (Hz) of 0.63, whereas AFLP primers identified approximately 147 fragments per primer with mean gene diversity of 0.25. A set of 54 SSR markers and 11 AFLP primers were identified as highly polymorphic (PIC ' 0.5 and 0.3 for SSR and AFLP, respectively), and suitable for molecular characterisation of germplasm. Principle co-ordinate analysis suggested that the AFLP and SSR loci could be used to discriminate between accessions collected from North Africa and Southern Europe from those collected from the Middle East. Both marker types indicate that accessions from North Africa and Southern Europe, the Middle East and Southern and Eastern Asia are genetically diverse. The results indicate the usefulness of the molecular markers to assess genetic diversity present within germplasm collections.