We report an investigation to establish the physical mechanisms responsible for decoherence in the generation of photon pairs from atomic ensembles, via the protocol of Duan et. al for long distance quantum communication [Nature (London) 414, 413 (2001)] and present the experimental techniques necessary to properly control the process. We develop a theory to model in detail the decoherence process in experiments with magneto-optical traps. The inhomogeneous broadening of the ground state by the trap magnetic field is identified as the principal mechanism for decoherence. In conjunction with our theoretical analysis, we report a series of measurements to characterize and control the coherence time in our experimental setup. We use copropagating stimulated Raman spectroscopy to access directly the ground state energy distribution of the ensemble. These spectroscopic measurements allow us to switch off the trap magnetic field in a controlled way, optimizing the repetition rate for single-photon measurements. With the magnetic field off, we then measure nonclassical correlations for pairs of photons generated by the ensemble as a function of the storage time of the single collective atomic excitation. We report coherence times longer than 10 microseconds, corresponding to an increase of two orders of magnitude compared to previous results in cold ensembles. The coherence time is now two orders of magnitude longer than the duration of the excitation pulses. The comparison between these experimental results and the theory shows good agreement. Finally, we employ our theory to devise ways to improve the experiment by optical pumping to specific initial states.
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