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The photoperiod is a major environmental factor in flowering control. Water spinach flowering under the inductive short-day condition decreases the yield of vegetative tissues and the eating quality. To obtain an insight into the molecular mechanism of the photoperiod-dependent regulation of the flowering time in water spinach, we performed transcriptome sequencing on water spinach under long- and short-day conditions with eight time points. Our results indicated that there were 6615 circadian-rhythm-related genes under the long-day condition and 8691 under the short-day condition. The three key circadian-rhythm genes, <i>IaCCA1</i>, <i>IaLHY</i>, and <i>IaTOC1</i>, still maintained single copies and similar <i>IaCCA1</i>, <i>IaLHY</i>, and <i>IaTOC1</i> feedback expression patterns, indicating the conservation of reverse feedback. In the photoperiod pathway, highly conserved <i>GI</i> genes were amplified into two copies (<i>IaGI1</i> and <i>IaGI2</i>) in water spinach. The significant difference in the expression of the two genes indicates functional diversity. Although the photoperiod core gene <i>FT</i> was duplicated to three copies in water spinach, only <i>IaFT1</i> was highly expressed and strongly responsive to the photoperiod and circadian rhythms, and the almost complete inhibition of <i>IaFT1</i> in water spinach may be the reason why water spinach does not bloom, no matter how long it lasts under the long-day condition. Differing from other species (<i>I. nil</i>, <i>I. triloba, I. trifida</i>) of the <i>Ipomoea</i> genus that have three <i>CO</i> members, water spinach lacks one of them, and the other two <i>CO</i> genes (<i>IaCO1</i> and <i>IaCO2</i>) encode only one CCT domain. In addition, through weighted correlation network analysis (WGCNA), some transcription factors closely related to the photoperiod pathway were obtained. This work provides valuable data for further in-depth analyses of the molecular regulation of the flowering time in water spinach and the <i>Ipomoea</i> genus.