Diplodia disease (Botryodiplodia theobromae) spread quite widely in Indonesia citrus center. Severe attacks of disease can cause death if it not controlled. The purpose of this study was determine the pathogenicity and the effect of toxins from three isolates of B. theobromae origin Pasuruan and Magetan on tangerine, pummelo, and sweet orange varieties. The study was conducted at Indonesian Citrus and Subtropical Research Institute during November 2015 – May 2016. This observation consisted of two experiments that pathogenicity test in screenhouse and crude toxin of patogen test in laboratory. Pathogenicity test used randomized block design arranged as factorial. The first factor was three isolates: Mg52A.1, Mg39.2 (from Magetan), Ps8b (from Pasuruan) and the second factor were kind of citrus (pummelo, tangerine , and sweet orange). The observation parameter consist of the incubation period, the number of necrotic samples and visual symptom. Crude toxin test treatment consists of a control test toxin without toxins, crude toxin Mg52A.1, crude toxin Mg39.2 toxin, crude toxin Ps8b. Application toxin carried out on the three leaf varieties of oranges. Each treatment was repeated three times and each consists of two leaves of different varieties. The results showed that the incubation period Mg39.2 isolates faster than two other isolates. Infection with different isolates and treatment of different citrus varieties shows that it did not different significantly in causing disease symptom of diplodia. Similarly result on crude toxin treatment with three isolates on three varieties showed that it were not different necrotic symptom. Thus the three isolates of pathogens B.theobromae origin from Pasuruan and Magetan have the same pathogenicity in causing disease symptoms in citrus pummelo, tangerine, and sweet orange. Toxin only play a role in accelerating the incubation period.