Fruit color is one of the most important external quality traits. Mutants with different color are useful for the study of regulating mechanism of coloration progress. A novel mutant, Fengwan, derived from Fengjie72-1 navel orange (Citrus sinensis L. Osbeck), has the distinctive characteristic of the coloration delay of 30 d or so, with the change in total soluble solid (TSS) and the ratio of TSS/acidity. In order to understand the mechanism underlying the difference of coloration between the mutant and the parental variety, the chlorophyll and carotenoid contents in the peel of two cultivars at different maturation stages were analyzed. The expression of genes responsible for some carotenoid biosynthetic enzymes (phytoene synthase, phytoene desaturase, zeta-carotene desaturase, beta-lycopene cyclase, beta-carotene hydroxylase) and chlorophyllase using the RT-PCR technique were also studied. The distinct decrease of chlorophyll in the peel of Fengwan navel orange occurred from early November to late November, about three weeks later than that of its original cultivar. Obvious accumulation of carotenoid in the peel of the mutant began on Dec.12, while that of the original cultivar began on Nov. 3. Analysis of independent-samples t-test showed that the chlorophyll content of the peel of Fengwan navel orange from October to November was significantly higher, and the carotenoid content from December to January was significantly lower than that in the peel of the parental line, Fengjie72-1 navel orange. The expression of chlorophyllase gene in the peel of Fengwan navel orange reached a maximum in January and kept at a slightly lower level from October to December than that of Fengjie 72-1 orange, while the time of gene expression about some carotenoid biosynthetic enzymes reaching a maximum in the peel of the mutant were one month later than that of the original cultivar.