The governing equations of a mathematical model describe how the values of the unknown variables (i.e. the dependent variables) change when one or more of the known (i.e. independent) variables change.
Physical systems can be modeled phenomenologically at various levels of sophistication, with each level capturing a different degree of detail about the system. A governing equation represents the most detailed and fundamental phenomenological model currently available for a given system.
For example, at the coarsest level, a beam is just a 1D curve whose torque is a function of local curvature. At a more refined level, the beam is a 2D body whose stress-tensor is a function of local strain-tensor, and strain-tensor is a function of its deformation. The equations are then a PDE system. Note that both levels of sophistication are phenomenological, but one is deeper than the other. As another example, in fluid dynamics, the Navier-Stokes equations are more refined than Euler equations.
As the field progresses and our understanding of the underlying mechanisms deepens, governing equations may be replaced or refined by new, more accurate models that better represent the system's behavior. These new governing equations can then be considered the deepest level of phenomenological model at that point in time.