The ingress of the fungus Alternaria alternata, which causes internal mold of ripe red pepper fruit without external signs of infection, was investigated. Information obtained in field surveys and inoculation experiments suggested that the fungus entered the developing fruit at the flowering stage via the stigma and the style. The fungus developed compact masses of mycelia and spores on seeds when the fruit was biologically mature. Infection by the parasite, damaged flower and young fruit tissues causing necrosis on the blossom end, on the seed, and placenta tissue. Hyperplasia of seed and placenta tissues was also observed. Fungal infection induced flower drop in greenhouse experiments. Disease incidence was affected by the age of the flower at the time of infection. The mode of ingress of A. alternata and the type of damage it causes to pepper fruit tissue under local conditions in Israel are unlike those reported by investigators in other countries.