We used a set of approximately 200 Arabidopsis thaliana (L.) Heynh. genes that are involved in the control of flowering time as a reference to identify orthologous (or homologous) counterparts of these genes in three legume species, that is, Lotus corniculatus L. var. japonicus Regel [syn. Lotus japonicus (Regel) K. Larsen], Medicago truncatula Gaertn. (barrel medic), and soybean [Glycine max (L.) Merr.]. A total of 96, 98, and 304 homologs of flowering genes were identified in L. corniculatus var. japonicus, M. truncatula, and G. max, respectively. Most of these genes were categorized into seven different flowering pathways, including photoperiod, vernalization, gibberellins, autonomous pathways, floral pathway integrators (FPIs), and floral meristem identity. Many key genes, including the FPI genes FT, SOC1, and LFY, are conserved in the legumes while CO, FRI, FLC, and FD were not. Eighteen genes were conserved as single copy genes in all three legume species, including GI, VRN2, COP1, and TSF. The chromosomal distribution of paralog-rich genes revealed differences in the major evolutionary processes affecting flowering genes in legumes, including whole genome duplication in soybean, tandem duplication in M. truncatula, and ectopic duplication in L. corniculatus var. japonicus. High divergence was observed among the members of large gene families, most containing transcription factors, indicating the accumulation of gene copies and gene divergence during evolutionary adaptations to environmental changes.