Microswimmers typically operate in complex environments. In biological systems, often diverse species are simultaneously present and interact with each other. Here, we derive a (time-dependent) particle-scale statistical description, namely a dynamical density functional theory, for such multi-species systems, extending existing works on one-component microswimmer suspensions. In particular, our theory incorporates the effect of external potentials, but also steric and hydrodynamic interactions between swimmers. For the latter, a previously introduced force-dipole-based minimal (pusher or puller) microswimmer model is used. As a limiting case of our theory, mixtures of hydrodynamically interacting active and passive particles are captured as well. After deriving the theory, we apply it to different planar swimmer configurations. First, these are binary pusher-puller mixtures in external traps. In the considered situations, we find that the majority species imposes its behavior on the minority species. Second, for unconfined binary pusher-puller mixtures, the linear stability of an orientationally disordered state against the emergence of global polar orientational order (and thus emergent collective motion) is tested analytically. Our statistical approach predicts, qualitatively in line with previous particle-based computer simulations, a threshold for the fraction of pullers and for their propulsion strength that lets overall collective motion arise. Third, we let driven passive colloidal particles form the boundaries of a shear cell, with confined active microswimmers on their inside. Driving the passive particles then effectively imposes shear flows, which persistently acts on the inside microswimmers. Their resulting behavior reminds of the one of circle swimmers, though with varying swimming radii. arXiv:1904.07277v2 [cond-mat.soft]