Cavendish banana (Musa AAA) shows green-ripening at high temperatures above 24 °C, while Bluggoe fruit (Musa ABB) turns completely yellow. To understand the genomic constitution of the fruit de-greening trait, we compared fruit ripening and chlorophyll (Chl) degradation in 4 banana cultivars, belonging to the Cavendish (AAA), Mysore (AAB), Pisang Awak (ABB) and Bluggoe (ABB) subgroups, at 30 °C and 20 °C. Compared with fruit at 20 °C, ripening progress of the 4 cultivars at 30 °C, as represented by the change in fruit firmness and expression of fruit ripening-related genes, ACS ACO and PG, was accelerated, while the de-greening of fruits was repressed in the AAA cultivar but enhanced in the 3 hybrids (AAB/ABB). The expression of Stay-Green 1 (SGR1), a key Chl degradation gene, was reduced in the AAA cultivar but induced in the hybrids, correlating to the fruit de-greening patterns. The A- and B-SGR1 alleles, from the A- and B-genome, respectively, and a recombinant of the two alleles (H-SGR1) were identified in the AAB/ABB cultivars. A highly conserved polymorphism code was found to differentiate the A/B/H-SGR1 alleles. Allele-specific expression analysis showed that the Bluggoe fruit transcribed only B-SGR1, while Pisang Awak and Mysore expressed B/H- and A/B-SGR1, respectively, and higher B-SGR1 transcription levels were detected at 30 °C than at 20 °C. Transient expression of A/B/H-SGR1 in tobacco leaves demonstrated that SGR1s were all targeted to chloroplasts, and A-SGR1 showed a weaker Chl degradation capacity than B/H-SGR1. The allelic imbalanced expression (AIE) of SGR1 was demonstrated to confer the different fruit de-greening traits to the AAA and AAB/ABB cultivars at high temperatures.