Mn-rich clusters in Mn-doped Ge thin films epitaxially grown on Ge (001) have been investigated by various transmission electron microscopy techniques. Both the mysterious Mn11Ge8 and the hexagonal Mn5Ge2 (a=0.72 nm and c=1.3 nm) clusters were confirmed to coexist in the thicker Ge0.96Mn0.04 film (80 nm). Their possible formation mechanism is attributed to the existence of ordered stacking faults. The fact that no Mn-rich clusters found in thinner films