Analysis of differential expression of closely related genes is a general problem. The lignin peroxidase genes of Phanerochaete chrysosporium represent a typical case. They are differentially expressed according to the conditions encountered during growth. We show that the expression of two such genes, LIG1 and LIG5, can be differentiated at the mRNA level using a highly specific form of the polymerase chain reaction. This generally applicable method allows rapid and accurate analysis of complex and closely related mRNA populations.