According to the Lambda Cold Dark Matter paradigm, the dark matter halos today were formed through successive mergers of smaller mass halos. Part of these merging halos survived without being disrupted in the merging event, and form the structure of galaxies and clusters today. We implement different models describing the properties of a population of substructures inside the Milky Way as well as at cosmological distances, based on recent N-body simulation. We also study the properties of the observed satellites of our Milky Way such as the dwarf galaxies, based on an hybrid modeling derived from astronomical data and numerical simulations. We present our predictions for the indirect detection of dark matter through the observation of gamma-rays produced in the annihilation process, in the case when the dark matter particle is the lightest supersymmetric particle. We study both the detectability of subhalos and their angular signatures. We also include the effect of the Sommerfeld enhancement of the annihilation cross section in the "slow", small mass galactic and extragalactic halos. We make predictions for both the Fermi telescope and for the Air Cherenkov Telescopes and show comparisons with the already available data.