Multi-season flowering is one of the most important traits of ornamental plants. In this study, the multi-season flowering candidate genes APETALA1 (AP1) and TERMINAL FLOWER1 (TFL1) in the multi-season flowering ‘Sijigui’ variety and autumn flowering ‘Jingui’ variety were compared and analyzed. Two homologous genes of AP1 were found in ‘Sijigui’ and ‘Jingui’, namely, OfAP1-a and OfAP1-b. OfAP1-a and OfAP1-b in ‘Sijigui’ and ‘Jingui’ both have full-length and intron-reserved splicing isoforms, resulting in the formation of four isoforms: OfAP1-a1 and OfAP1-a2, and OfAP1-b1 and OfAP1-b2. The TFL1 gene has only one homologous gene in ‘Sijigui’ and ‘Jingui’, named OfTFL1. It has two isoforms in ‘Sijigui’ and ‘Jingui’. One is the normal transcript isoform OfTFL1-1; and the other is the OfTFL1-2 isoform produced by the addition of 2bp base in the first exon. No differences were observed in the sequence and protein structure of the isoforms of OfAP1 and OfTFL1 in both varieties. However, the expression patterns of OfAP1-a1, OfAP1-a2, OfAP1-b1, OfAP1-b2, and OfTFL1-2 during autumn flower bud differentiation in ‘Sijigui’ and ‘Jingui’ were different. In this study, we first found the isoforms for the candidate genes of multi-seasonal flowering, AP1 and TFL1, in ‘Sijigui’ and ‘Jingui’ varieties. Our study will provide useful genetic resources for further study on the multi-season flowering mechanism in sweet osmanthus.