Endopolygalacturonases (endoPGs) are fungal enzymes secreted during the infection in order to degrade plant cell wall pectins. In Fusarium spp., endoPGs are among the first enzymes produced during infection and play a crucial role in plant tissue penetration and colonization. The endoPG of F. phyllophilum strain FC-10, previously classified as F. verticillioides, is the best characterized Fusarium cell wall degrading enzyme. In this work we have carried out a phylogenetic analysis of the endoPG (pg) gene sequence that confirms the classification of the FC-10 strain as F. phyllophilum, and also shows an unexpected divergence of the pg gene of F. phyllophilum strain NRRL 25305. This gene and the biochemical characteristics of the encoded product appear more closely related to those of F. verticillioides pg. This observation and the evidence that endoPGs have experienced positive selection indicate that selective pressure acting on these enzymes may limit the use of their gene sequences as reliable markers for phylogenetic studies.