Two different decoding methods of an all-optical chaotic communication system are investigated when chaotic modulation (CM) encoding format is employed. The transmitter consists of an external cavity semiconductor laser generating, thus, a chaotic carrier, modulated using an external modulator. The receiver is either a solitary semiconductor laser diode identical to that of the transmitter or a laser diode coupled to an external cavity, forming an open- or a closed-loop configuration, respectively. The performance of the system is then evaluated by means of calculating the Q-factor extracted by the eye diagram of the recovered data when two different approaches of the decoding process for the receiver are adopted. The first decoding method relies on the widely proposed, normalized to the receiver's amplitude output, difference of the two lasers' optical amplitude outputs, while the second one corresponds to a more realistic case by subtracting the electrical current outputs of two p-i-n photodiodes coupled to the transmitter and receiver laser correspondingly. By comparing the numerical results extracted by the two decoding methods and for various cases of interest, such as employing open- or closed-loop configuration for several message bit rates and different lasers' driving current, it will be shown that, under certain circumstances, the two decoding methods result in significantly different results.