Tree peony (Paeonia suffruticosa) ‘Luoyang Hong’, a typical purplish red-flowered cultivar, is particularly appreciated by Chinese among the hundreds of cultivars. However, in-vase ‘Luoyang Hong’ flowers do not exhibit natural flower color as shown by on-tree flowers, since color fading of in-vase flowers is easily observed with the naked eye. This study was carried out to reveal the underlying molecular mechanism of color fading of in-vase P. suffruticosa ‘Luoyang Hong’. Five regulatory genes and six structural genes involved in anthocyanin biosynthesis were isolated based on a transcriptome library from P. suffruticosa ‘Luoyang Hong’ petals. Compared with fully opened on-tree flowers in field conditions, in-vase flowers (vase condition of 21–23°C, 50–60% RH and a 16h photoperiod with an illumination of ∼40μmolm−2s−1) of P. suffruticosa ‘Luoyang Hong’ at full opening stage show significant color fading with 50.20% greater lightness, 37.43% less redness and 36.18% lower chroma in non-blotch parts of the middle petals (the 4th to 6th layer petal). From pre-opening to full opening stage, anthocyanin contents in inner, middle and outer petals of in-vase flowers was 24.49–38.75% lower than those in on-tree developing flowers. With the exception of PsCHI1, another ten anthocyanin biosynthetic genes were preferentially and highly expressed in floral tissues (sepals, petals, stamens or carpels). Temporal expression analysis of anthocyanin biosynthetic genes in on-tree and in-vase developing flowers revealed that only the expression pattern of PsF3′H1 was correlated with anthocyanin content development. On the whole, PsbHLH3, PsWD40-1, PsWD40-2, PsMYB2, PsCHS1, PsF3H1 and PsDFR1 of P. suffruticosa ‘Luoyang Hong’ showed lower transcript abundances in in-vase flowers than in on-tree flowers, suggesting that the low expression of these genes is probably responsible for lower anthocyanin contents, resulting in the color fading in the petals in in-vase flowers.