We are interested in controlling strobili production in Cryptomeria japonica D. Don by genetic engineering. However, details of the molecular mechanisms governing reproduction in gymnosperms have not been documented. In this study, we characterized the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1)-like (CjMADS15) and AGAMOUS-LIKE 6 (AGL6)-like (CjMADS14) MADS-box genes of C. japonica. Their expression patterns differed in that CjMADS15 was expressed in all organs except pollen, and was especially expressed in needles, stems and strobili, whereas CjMADS14 was expressed mainly in male and female strobili. Furthermore, gibberellic acid (GA(3))-induced expression of CjMADS14 and CjMADS15 also differed; expression of CjMADS15 increased within a week of GA(3) treatment, whereas expression of CjMADS14 increased within 1 month. Both genes had the potential to induce early reproduction, because transgenic Arabidopsis that ectopically expressed CjMADS14 or CjMADS15 flowered earlier than wild-type plants. When we overexpressed a fusion of CjMADS14 to a transcriptional repression domain (SRDX) from SUPERMAN under control of the cauliflower mosaic virus (CaMV) 35S promoter (35S), the flowering time of transgenic Arabidopsis with the 35S::CjMADS14:SRDX construct was comparable with that of 35S::CjMADS14. Thus, CjMADS14 and CjMADS15 play important roles during the development of male and female strobili in C. japonica. Our finding will contribute to elucidate the molecular mechanisms for the formation of reproductive organs in gymnosperms.