A new modulation technique for Continuous Wave (CW) Lidar is presented based on Binary Phase Shift Keying (BPSK) using orthogonal carriers closely spaced in frequency, modulated by Maximum Length (ML) sequences, which have a theoretical autocorrelation function with no sidelobes. This makes it possible to conduct multi-channel atmospheric differential absorption measurements in the presence of thin clouds without the need for further processing to remove errors caused by sidelobe interference while sharing the same modulation bandwidth. Flight tests were performed and data were collected using both BPSK and linear swept frequency modulation. This research shows there is minimal or no sidelobe interference in the presence of thin clouds for BPSK compared to linear swept frequency with significant sidelobe levels. Comparisons between of CO(2) optical depth Signal to Noise (SNR) between the BPSK and linear swept frequency cases indicate a 21% drop in SNR for BPSK experimentally using the instrument under consideration.