We show that the self-assembly of monodisperse CdSe nanocrystals synthesized at lower temperature (∼310 °C) into three-dimensional supercrystals results in the formation of separate regions within the supercrystals that display photoluminescence at two distinctly different wavelengths. Specifically, the central portions of the supercrystals display photoluminescence and absorption in the orange region of the spectrum, around 585 nm, compared to the 575 nm photoluminescence maximum for the nanocrystals dispersed in toluene. Distinct domains on the surfaces and edges of the supercrystals, by contrast, display photoluminescence and absorption in the green region of the spectrum, around 570 nm. We attribute the different-colored domains to two subpopulations of NCs in the monodisperse ensemble: the nanocrystals in the "orange" regions are chemically stable, whereas the nanocrystals in the "green" regions are partially oxidized. The susceptibility of the "green" nanocrystals to oxidation indicates a lower coverage of capping molecules on these nanocrystals. We propose that the two subpopulations correspond to nanocrystals with different surfaces that we attribute to the polytypism of CdSe.