  A new supersymmetric approach to the analysis of dynamical symmetries for
matrix quantum systems is presented. Contrary to standard one dimensional
quantum mechanics where there is no role for an additional symmetry due to
nondegeneracy, matrix hamiltonians allow for non-trivial residual symmetries.
This approach is based on a generalization of the intertwining relations
familiar in SUSY Quantum Mechanics. The corresponding matrix supercharges, of
first or of second order in derivatives, lead to an algebra which incorporates
an additional block diagonal differential matrix operator (referred to as a
"hidden" symmetry operator) found to commute with the superhamiltonian. We
discuss some physical interpretations of such dynamical systems in terms of
spin 1/2 particle in a magnetic field or in terms of coupled channel problem.
Particular attention is paid to the case of transparent matrix potentials.
