The emergence of flowering disorder, specifically the bud break disorder observed in flower buds, has become a serious problem for Japanese pear 'Kosui' greenhouse production in southern Japan. To understand the mechanism behind this problem, the expression of genes related to endodormancy and flowering were investigated in "flowering disorder trees" (FDTs). In 2017 and 2019, remarkably warm temperatures were recorded during the winter season, and the degree of flowering disorder in FDTs was severe. Forced cultivation experiments suggested that endodormancy of "normal trees" (NTs) was released well before fulfilling the chilling requirement (CR), suggesting that 'Kosui' trees grown in greenhouses had a short endodormancy period. We also found that the dormancy depth of FDTs was shallower than that of NTs before and after fulfilling the CR, whereas FDTs entered a deeper dormancy when the greenhouse was covered by a plastic film during the ecodormancy period, suggesting that FDTs' dormancy progression was significantly different from that of NTs during endodormancy and ecodormancy. Gene expression analysis showed that the expression level of the endodormancy-related gene, MADS13-3, was correlated with dormancy depth in NTs, but not in FDTs. Additionally, the expression levels of the putative flowering regulator, PpFLC3-like gene, were significantly lower in FDTs than in NTs in December, before fulfilling the CR. Additionally, the flowering promoter, PpFT, was also significantly lower in FDTs than in NTs in March after fulfilling the CR. The survey years 2017 and 2019 were warm winters with a high mean temperature difference from the climatological normal in December. These results suggest that the flowering disorder of greenhouse-cultivated 'Kosui' is related to the shallow dormancy depth and/or inappropriate dormancy and flowering progression during endodormancy and ecodormancy, especially when flower buds encounter high temperatures during dormancy.