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Timely flowering is a determinative trait for many economically valuable species in the <i>Dendrobium</i> genus of the Orchidaceae family, some of which are used for ornamental and medicinal purposes. <i>D. nobile</i>, a representative species of nobile-type <i>Dendrobium</i>, normally flowers in spring after exposure to sufficient low temperatures in winter. However, flowering can be stopped or disrupted by the untimely application of high temperatures. Little is known about the regulation and the mechanisms behind this switch. In this study, we report two isoforms from the KFK09_017173 locus of the <i>D. nobile</i> genome, named <i>DnFCAγ</i> and <i>DnFCAβ</i>, respectively, that cooperatively regulate flowering in <i>D. nobile</i>. These two isoforms are generated by alternative 3′ polyadenylation of <i>DnFCA (FLOWERING CONTROL LOCUS C in D. nobile)</i> pre-mRNA and contain a distinct 3′-terminus. Both can partially rescue late flowering in the <i>Arabidopsis fca</i>-<i>1</i> mutant, while in wild-type <i>Arabidopsis</i>, they tend to delay the flowering time. When introduced into the detached axillary buds or young seedlings of <i>D. nobile</i>, both were able to induce the transcription of <i>DnAGL19</i> (<i>AGAMOUS LIKE 19 in D. nobile)</i> in seedlings, whereas only <i>DnFCAγ</i> was able to suppress the transcription of <i>DnAPL1 (AP1-LIKE 1 in D. nobile)</i> in axillary buds. Furthermore, the time-course change of <i>DnFCAγ</i> accumulation was opposite to that of <i>DnAPL1</i> in axillary buds, which was remarkable under low temperatures and within a short time after the application of high temperatures, supporting the suggestion that the expression of <i>DnAPL1</i> can be inhibited by a high accumulation of <i>DnFCAγ</i> in floral buds. In leaves, the accumulation of <i>DnFCAβ</i> was in accordance with that of <i>DnAGL19</i> and <i>DnFT</i> (<i>FLOWERING LOCUS T in D. nobile)</i> to a large extent, suggesting the activation of the <i>DnAGL19–DnFT</i> pathway by <i>DnFCAβ</i>. Taken together, these results suggest that the DnFCAγ–DnAPL1 pathway in axillary buds and the DnFCAβ–DnAGL19 pathway in the leaves cooperatively promote flowering under low temperatures. The long-term and constant, or untimely, application of high temperatures leads to the constitutive suppression of <i>DnAPL1</i> by a high level of <i>DnFCAγ</i> in axillary buds, which consequently delays floral development.