Whiteflies (Homoptera: Aleyrodidae) have endosymbiotic organisms, Gamma subdivision of the class Proteobacteria, in their digestion system. These organisms have important role in survival and reproduction of their hosts, therefore the ultrastructure of them was examined in Bemisia tabaci Gennadius, using transmission electron microscopy. Two types of microorganisms were observed in mycetocytes. The predominant type lacked a distinct cell wall, was pleomorphic in shape with a surrounding vacuole. The second type was a convex organism, with the distinct cell membrane, and often found in group of varying number within vacuoles. Different populations of B. tabaci were collected from Isfahan, Fars, Kerman, Tehran, Khorasan, and Azarbayjan provinces for studying of the correlation between mycetocyte morphological variation and populations or biotypes of B. tabaci.B. tabaci individuals from Isfahan, Fars, and Kerman contained two morphological types of microorganisms. In contrast, individuals from populations of Tehran, Khorasan, and Azarbayjan consistently contained three distinct morphological types of microorganisms within their mycetocytes.Since the third type of microorganisms are present only in A biotype of B. tabaci, and B biotype contains only two of mentioned microorganisms. Biotype B of B. tabaci which is more destructive than the A one, exists in Isfahan, Fars, Kerman, and probably other southern regions of Iran.