We have recently shown that in II-VI/III-V heterojunctions and related devices fabricated by molecular beam epitaxy, the II/VI flux ratio employed during the early stages of II-VI growth can be used to control the local interface composition and the band alignment. Here we demonstrate that the local interface composition in pseudomorphic, strained ZnSe/GaAs(001) heterostructures as well as lattice-matched ZnSe/In0.04Ga0.96As(001) heterostructures also have a dramatic effect on the nucleation of native stacking fault defects. Such extended defects have been associated with the early degradation of blue-green lasers. We found, in particular, that Se-rich interfaces consistently exhibited a density of Shockley stacking fault pairs below our detection limit and three to four orders of magnitude lower than those encountered at interfaces fabricated in Zn-rich conditions.