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Self-incompatibility (SI) is a genetic mechanism in angiosperms that prevents selfing. The SI system in passion fruit (Passiflora edulis Sims) was investigated using hand pollinations. Pollen tube growth was inspected by microscopy, and sequence analysis of potential regulators of this process was carried out. The results revealed that the pollen tubes grew slowly and were often completely arrested in the stigma in an incompatible combination. Under these circumstances the pollen tube was rapidly and significantly rearranged, followed by the rapid deposition of callose in the stigma during the SI response. The structural changes in the pollen grain after an incompatible pollination were investigated using scanning electron microscopy. Furthermore, ultrastructural observations during incompatible interactions showed that the membrane system of the pollen tube was damaged, and fertilisation was not observed or was considerably delayed when compared to compatible interactions. The analysis presented here provides evidence that the passion fruit genome presents similar sequences to those encoding factors involved in SI in different species. These results suggest that, in the SI system of passion fruit, the rejection of an incompatible pollen grain is characterised by drastic structural changes in both pollen and pollen tube.