The radical intermediates formed upon catalytic or photooxidation of the carotenoid 9'-cis neoxanthin inside MCM-41 molecular sieves were detected by pulsed Mims and Davies electron nuclear double resonance (ENDOR) spectroscopies and characterized by density functional theory (DFT) calculations. Mims ENDOR spectra (20 K) were simulated using the hyperfine coupling constants predicted by DFT, which showed that a mixture of carotenoid radical cations (Car(+)) and neutral radicals (#Car) is formed. The DFT relative energies of the neutral radicals formed by proton loss from the C5, C5', C9, C9', C13, and C13'-methyl groups of Car(+) showed that #Car(9') is energetically most favorable, while #Car(9), #Car(13), #Car(13'), #Car(5'), and #Car(5) are less favorable for formation by 2.6, 5.0, 5.1, 22.5, and 25.6 kcal/mol. No evidence for formation of #Car(5') and #Car(5) was observed in the EPR spectra, consistent with DFT calculations. The epoxy group at the prime end and the allene bond at the unprime end prevent protons loss at the C5 and C5'-methyl groups by reducing the conjugation so crucial for the neutral radical stability. Previous CV measurements for allene-substituted carotenoids show that once the radical cations are formed, proton loss is rapid. These examined properties and the known crystal structure of the light harvesting complex II (LHC II) suggest the absence of the neutral radicals of 9'-cis neoxanthin available for quenching the excited states of Chl, consistent with its observed nonquenching properties.