[Fungus] Septoria citri Pass.
Septoria spot
Septoria has saprophytic capabilities and pycnidia often form on dead twigs and leaves. Conidia from these pycnidia are spread by splashing water and may infect leaves and fruit. However, symptoms may not result for up to six months after infection.
Leaf - foliar lesions are blister-like, raised, black and 1-4 mm in   diameter. Over time the center of the lesions become necroticnecrotic:
           a cell, group of cells, or tissue that has suffered a rapid destruction   and quick death; typically localized and may be caused by injury, radiation,   chemicals, toxic substances, or microbiological interactions  
 and pale   brown. Pycnidia develop in the lesions especially following leaf drop when   the lesionlesion:
           any defined area of living tissue that has been structurally modified as   a result of a disease or damaging process  
 turns dark brown with dark margins. When conditions are   favorable, the disease may cause severe leaf drop in the lower portion of the   tree.
Fruit - early fruit lesions are small light tan to reddish brown pits 1-2 mm in diameter that extend no deeper than the flavedo. Older lesions are darker sunken 20-30 mm in diameter. Dark fruiting bodies, pycnidia, may develop in these lesions. Lesions may appear in the form of "tear stains" patterns. Spots are more evident on ripe fruit.
All citrus cultivarcultivar:
           deliberately selected variants within a cultivated species that are grown for   horticultural and/or agricultural advantages  
 are susceptible.  However, Valencia oranges, Navel oranges, lemons and grapefruit are frequently damaged. 
This disease has been reported from most citrus producing areas throughout the world.