Small scale tests of the nature of dark matter require simulations which incorporate baryonic physics. In this thesis we study how the inclusion of baryonic physics affects the abundance and properties of dark matter halos and their substructures. We introduce a new high-resolution hydrodynamical zoom simulation of a 10^13 Msun galaxy group, which we use to study the properties of halos and subhalos relevant to strong lensing tests of the cold dark matter model. We also compare two hydrodynamical simulations of Milky Way-mass halos, Apostle and Auriga. We find that the number of subhalos, as well as the slope of the subhalo mass
function and the subhalo velocity distribution, is altered significantly depending on the implementation of baryonic physics
