The symptoms and the fact that the disease affects immature fruit on the tree are suggestive of Phytophthora. However, Penicillium is present on the older lesions. The easiest way to distinguish between the two is to press the lesion before you see a lot of hyphae on the outside. Phytophthora (brown rot) lesions are quite firm – you finger won’t go into it. Phytophthora also has a quite strong aromatic smell. If the lesion is soft and wet (a soft rot) and your finger goes in easily then it is probably not Phythphthora. Basic, but it works! None of the Penicillium species were known to affect young fruit on the tree. Normally, it is found on trees only when fruit mature or become over mature and it is normally associated with injury such as bird damage. Possibly, there are initial infections by Phytophthora, followed by Penicillium. To be sure, there is need to isolate from the lesion margin onto a standard medium such as PDA with antibiotics and also onto a Phytophthora selective medium.

Another possibility is that the fruit has been attacked by the nocturnal fruit-piercing moth, Gonodonta sp. If the damage occurs suddenly and close to harvest when the sugars are starting to build up, it may well be one of the larger species of fruit piercing moth. It is very common on citrus in the humid tropics, especially if there is forest nearby. Go out to the affected trees with a torch and shine it on the trees. The moths have bright red eyes that reflect the light and are easy to see. The wounds rot quickly with a range of fungal and bacterial organisms. Squeeze the fruit gently, ooze may come out of the incision made by the moth.