Among star-forming galaxies there is a particular population whose spectra exhibit strong nebular emission lines. Such features are generated by young, massive stars ionising the surrounding particles of the gas, which subsequently release high-energy UV photons. These emission line galaxies (ELGs) will be the preferred targets of new-generation spectroscopic surveys as Euclid, DESI, WFIRST, 4MOST, J-PAS and Subaru PFS. All these instruments will observe [OII], [OIII] and Hα ELGs out to redshift z~2 to trace the cosmic star formation history and to understand the galaxy formation and evolution mechanisms. Near-future surveys will enable us to build 3D maps of the Universe with unprecedented accuracy to probe its large scale structure and to unveil the nature of dark energy. Therefore, it is crucial to understand how to best measure and precisely model the clustering properties of such galaxies and how they occupy and interact with their host dark matter halos. We address these issues by analysing state-of-the-art data using large-volume, high-resolution, cosmological simulations and semi-analytic models of galaxy formation to prepare the clustering prospects for the new generation of optical and near-IR experiments.