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Line intensity mapping (LIM) is an emerging observational method to study the large-scale structure of the Universe and its evolution. LIM does not resolve individual sources but probes the fluctuations of integrated line emissions. A serious limitation with LIM is that contributions of different emission lines from sources at different redshifts are all confused at an observed wavelength. We propose a deep learning application to solve this problem. We use conditional generative adversarial networks to extract designated information from LIM. We consider a simple case with two populations of emission line galaxies; H$\rmα$ emitting galaxies at $z = 1.3$ are confused with [OIII] emitters at $z = 2.0$ in a single observed waveband at 1.5 $\rmμ$m. Our networks trained with 30,000 mock observation maps are able to extract the total intensity and the spatial distribution of H$\rmα$ emitting galaxies at $z = 1.3$. The intensity peaks are successfully located with 74% precision. The precision increases to 91% when we combine the results of 5 networks. The mean intensity and the power spectrum are reconstructed with an accuracy of $\sim$10%. The extracted galaxy distributions at a wider range of redshift can be used for studies on cosmology and on galaxy formation and evolution.