We use a galaxy formation model to study the nature and evolution of emission line galaxies. In particular, we focus on the properties of Ly-alpha and H-alpha emitters, due to their many cosmological applications being considered for current and future observational studies. By combining a semianalytical model with a large N-body simulation we predict the clustering of Ly-alpha emitters. With increasing redshift, Ly-alpha emitters are found to trace progressively rarer, higher density regions of the Universe. We measure the clustering of Ly-alpha emitters by constructing mock catalogues of surveys finding a good agreement between the model and the observational measurements. Furthermore, we use the mock catalogues to study the sample variance of current and forthcoming Ly-alpha surveys. Current surveys should be extended significantly in solid angle to allow a robust measurement of the clustering of Ly-alpha emitters, particularly at z>8. On the other hand, future space-based galaxy surveys will map the galaxy distribution using H-alpha emitters or H-band selected galaxies at 0.5