There have been several reports on the effects of various photoperiods on flowering in Capsicum annuum, but few on such effects on other species of the genus Capsicum. In this study, the flowering under various photoperiods of two C. frutescens lines from the Bonin and Ryukyu Islands in Japan and C. annuum cv. ‘Takanotsume’ (referred as BON, RYU, and TK, respectively) was investigated. The main differences in flowering between C. frutescens and C. annuum were evident under long-day photoperiods. TK plants grown under photoperiods longer than 15 h bore flowers normally, whereas BON and RYU plants grown under the same conditions did not bear flowers at first, because their buds failed to grow, and eventually aborted. BON plants bore flowers under a 24-h photoperiod, although the time to flowering was much longer than that for TK plants, but RYU plants exposed to photoperiods longer than 14 h bore no flowers during the entire experimental period. Therefore, long-day photoperiods strongly inhibit C. frutescens flower bud growth, and there are interspecific differences in flowering between C. frutescens and C. annuum and intraspecific differences in flowering between the two C. frutescens genotypes.