In recent years, substantial progress has been made in understanding the role of cell wall-degrading enzymes in virulence of fungal pathogens using genetic tools. A homologous recombination-mediated targeted gene disruption of a single pectolytic gene decreased virulence in multiple fungal pathogens. Furthermore, differential regulation of a gene that encodes a cell wall-degrading enzyme during infection under different host environments has recently been examined, and host pH and sugars are involved in the regulation of the polygalacturonase gene. We will provide a brief overview of the biology of the macerating diseases caused by phytopathogenic Alternaria pathogens in particular hosts, followed by a description of possible mechanisms controlling the differential expression of genes encoding cell wall-degrading enzymes in the infected host.