In this paper, we analyze the performance of code acquisition system in atmospheric optical code division multiple access (OCDMA) communications using optical orthogonal codes. Memory introduced by temporal correlation of optical fading process precludes us from using the Markov chain model for a code acquisition analysis. By considering this issue, we discuss how to extend the applicability of the Markov chain model to the atmospheric OCDMA communications. We analyze and compare the performance of correlator and chip level detector (CLD) structures in the acquisition system. In our analysis, we consider the effects of free space optical channel impairments, multiple access interference, and receiver thermal noise in the context of semi-classical photon-counting approach. Furthermore, we evaluate the performance of various two stage schemes that utilize different combinations of active correlator, matched filter, and CLD in search and verification stages, and we find the optimum acquisition scheme among them. Numerical results show significant improvement in reducing the acquisition time and required power for synchronization using our optimum scheme in the wireless OCDMA communications.