The Hamiltonian description of classical gauge theories is a very well studied subject. The two best known approaches, namely the covariant and canonical Hamiltonian formalisms, have received a lot of attention in the literature. However, a full understanding of the relation between them is not available, especially when the gauge theories are defined over regions with boundaries. Here, we consider this issue, by first making it precise what we mean by equivalence between the two formalisms. Then, we explore several first-order gauge theories and assess whether their corresponding descriptions satisfy the notion of equivalence. We shall show that, even when in several cases the two formalisms are indeed equivalent, there are counterexamples that signal that this is not always the case. Thus, non-equivalence is a generic feature of gauge field theories. These results call for a deeper understanding of the subject.