We study master equations of the form $$(\partial_t+L)^su=f\quad\hbox{in}~\mathbb{R}\timesΩ$$ where $L$ is a divergence form elliptic operator and $Ω\subseteq\mathbb{R}^n$. These are nonlocal equations of order $2s$ in space and $s$ in time that take into account the values of $u$ everywhere in $Ω$ and for past times. We show parabolic interior and boundary Harnack inequalities and local parabolic Hölder continuity of solutions. To this end, we prove a characterization of fractional powers of parabolic operators $\partial_t+L$ with a degenerate parabolic extension problem.