Physiological fruit drop in citrus is the deeper problem for fruit production and many researches have suggested that decreasing of carbohydrate translocation to fruit involved in fruit abscission. The fruit abscission process requires 3 stages for successful abscission, which include "induction", "decision", and "execution". However, there is almost no information in the molecular mechanism of secondary physiological fruit drop in citrus. Here, anatomical observation and microarray analysis demonstrated the candidate genes involved in the fruit abscission process after induction of fruit abscission by incubating the detached ponkan (Citrus reticulata Blanco) and hyuganatsu (C. tamurana hort. ex Tanaka) fruit on agar medium. In our study, the cumulative ratio of fruit abscission was very high in ponkan, but very low in hyuganatsu. Morphology of abscission zone (AZ) cells was drastically changed in ponkan, but almost not changed in hyuganatsu. From the 60 K microarray analysis at 0, 12, 24, or 36 h after the induction, the specific up-regulated genes in ponkan AZ tissue were identified. The expressions of many cell wall degrading related genes, such as beta-galactosidase, polygalacturonase and beta-glucosidase etc. increased rapidly at 24 h. These results indicated that "execution" stage of fruit abscission process would be initiated until 24 h after the induction of fruit abscission in citrus.