Cucumber mosaic virus (CMV) causes serious diseases in agricultural crops worldwide, predominantly in vegetable and ornamental plants. A critical interaction has been reported between the plant Ferredoxin I (Fd I) protein with the coat protein (CP) of the M strain of CMV (M-CMV) but not by the CP of the Q strain of CMV (Q-CMV). To ascertain the most likely symptom development model based on CMV CP interacting with the plant Fd I protein, further in silico investigation was performed on the CPs of the strains Q-CMV and M-CMV. The biological assembly of the CMV CP in virions is composed of hexameric and pentameric units. The results showed that there were significantly different interactions between pentameric and hexameric forms of M and Q-CMV CPs with Fd I. Pentameric structural forms of M-CMV CP interact strongly with Fd I compared to pentameric structures of Q-CMV CP, while there were no significant differences in the affinities of hexameric structures for Fd I between M and Q-CMV CPs. it can be deduced that probably pentameric structures of M-CMV CP block activation of plant Fd I protein. Therefore, it could be hypothesized that trapping Fd I in the complex of pentameric structures can lead to inhibition of the activity of plant Fd I in the photosynthetic electron transport chain leading the severe symptom development seen in M-CMV infected plants but not in Q-CMV infected plants. It seems likely that any factor that inhibits the interaction of CMV CPs with plant Fd I can prevent this symptom development.