Molecular markers linked to loci of interest can be used for fine mapping a particular area of a genome or for marker-assisted selection. We present an approach for screening individual plants with polymorphic markers that facilitates phenotyping in large populations. Polymorphic DNA fragments, amplified by PCR, are labelled with digoxigenin and used as probes on slot blots of amplified DNA from the individual plants to be tested. DNA is obtained by a simple two-tube purification method. The colorimetric detection of alleles on the blots is more reliable, and more amenable to automation, than conventional staining of electrophoresis gels.Key words: molecular markers, RAPD, genetic mapping, breeding.