The switch from vegetative to reproductive growth is a major developmental transition in flowering plants, which depends on the balanced expression of the genes within a complex network that is controlled by both environmental and endogenous factors. Molecular regulation of flower development has been investigated extensively in model plants, particularly Arabidopsis. However, little is known about the mechanisms that regulate flowering in lotus. To analyse the molecular regulation of flowering in lotus, comparative transcript profiling was performed at two stages of bud development – the initial developmental stage (T1) and the fast developing stage (T2) – in the lotus cultivars ‘BG’ (B, temperate lotus) and ‘WR1’ (W, tropical lotus). A total of 140 504 368 high-quality 100-bp reads were obtained and aligned against the lotus reference genome. Of the 23 361 genes assembled, at least 88% of these transcripts were detected in each sample. These genes were significantly enriched in 40 Gene Ontology terms and 236 Kyoto Encyclopedia of Genes and Genomes pathways. Further comparisons of the transcripts in the four libraries revealed that 1808, 1330, 785, 702, 1954, and 2050 genes were differentially expressed between BT1 and BT2, WT1 and WT2, BT1 and WT1, BT2 and WT2, BT1 and WT2 and BT2 and WT1 samples, respectively. Analysis of the four libraries identified 147 lotus flowering-time genes homologous to genes that control flowering-time pathways in other plants. Differential regulation of the COP1, CCA1, LHY, CO-LIKE, VIN3, GAI, and FT genes, which participate in the photoperiod, vernalization and gibberellic acid pathways, suggested that they might control the early flowering of lotus. The extensive transcriptome dataset should provide a foundation for comparative gene expression studies on the regulation of flowering in lotus. Comparative transcriptomic analysis detected several differentially expressed genes and potential candidate genes required for early flowering in lotus. These results provide new insight into the molecular mechanisms that regulate flowering in lotus.