Whereas CdSe nanorods that are grown in organic solution have a hexagonal wurtzite structure, which is the limiting case for exchange, HgSe is more commonly encountered as a cubic zinc blende system. An exchange process was performed at room temperature and at atmospheric pressure in an aqueous environment after phase transfer of the original CdSe nanorods, which reinforced the tendency for the endpoint of HgSe to be cubic. Consequently, we observed that under ambient conditions, the exchange process terminated with an average composition of only Cd0.9Hg0.1Se. Following the changes during the process by optical spectroscopy and high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM), we observed that the Hg2+ ions diffused into the rods to a point limited by the formation of stacking faults due to the different lattice structures of the two limiting cases of zinc blende and wurtzite. HAADF-STEM and energy dispersive spectroscopy analyses also confirmed that the Hg substitution did not occur uniformly throughout the individual nanorods, as Hg-poor and Hg-rich regions coexist around the stacking faults. The formation of near-infrared-emitting alloyed CdxHg1−xSe nanorods in an aqueous medium highlights the subtle dependence of the ion-exchange process on the differences in the crystal structures of the two endpoint lattices.