The different procedures used for molecular genotyping of ECM root tips and evaluation of the phylochip. DNA was extracted from individual ECM root tips or from pooled ECM root tips and subjected to PCR amplification to produce specific ECM ITS sequence or a heterogeneous mixture of ITS sequences, respectively. Individual ITS sequences were directly sequenced. The heterogeneous mixture of ITS sequences (ITS clone libraries) were either separated into individual molecules by cloning in bacterial plasmids or used directly for microarray hybridisation. The results of these three different technical approaches were analysed and compared. In addition, to test the specificity of the spotted oligonucleotides, the phylochips were hybridised with a heterogeneous mixture of ITS sequences from identified fungal sporocarps.