The circadian—or biological—clock is an intrinsic, timekeeping, molecular mechanism that allows plants to coordinate physiological activities over 24-hour cycles called circadian rhythms. Photoperiodism is a collective term for the biological responses of plants to variations in the relative lengths of dark and light periods. The period of light-exposure is called the photoperiod.

One example of photoperiodism in plants is seasonal flowering. Scientists believe that plants are cued to flower by the correspondence of their circadian clocks to changes in the photoperiod. They detect these changes using light-sensitive photoreceptor systems.

Phytochromes are a group of photoreceptors involved in flowering and other light-mediated processes. The phytochrome system enables plants to compare the duration of dark periods over several days.

Short-day (long-night) plants flower after a minimum number of consecutive long nights. Long-day (short-night) plants, by contrast, initiate flowering following a minimum number of consecutive short nights.

Phytochromes exist as two interconvertible forms: Pr and Pfr. Pr is converted into Pfr during the day, so Pfr is more abundant in daylight hours. Pfr is converted into Pr at night, so there is more Pr at nighttime. Therefore, plants can determine the length of the day-night cycle by measuring the Pr/Pfr ratio at dawn. The long nights of winter reduce Pfr levels at dawn, while the shorter nights of spring result in higher Pfr levels at sunrise.