The expression of ftsZ, encoding the initiating protein of the prokaryotic cell division was analysed in natural Prochlorococcus populations in the Gulf of Aqaba, northern Red Sea. During the seasonal Prochlorococcus bloom in September 2000, picoplankton was collected from the deep chlorophyll maximum (DCM) at 2–4 h intervals over 3 consecutive days. Flow cytometric measurements as well as DNA sequence analyses showed that Prochlorococcus was the dominant photosynthetic organism. Cell densities peaked as high as 1.4 × 105 cells ml−1. This DCM population mainly consisted of brightly red fluorescing Prochlorococcus cells, corresponding to low light-adapted ‘ecotypes’ (sensu Moore et al., 1998, Nature 393: 464–467). Prochlorococcus populations grew in a highly synchronized fashion with DNA replication in the afternoon and cell division during the night. The ftsZ mRNA level reached maximum values within the replication phase between 14.00 and 16.00 hours, and minimum values between 02.00 and 06.00 hours. Thus, the transcriptional regulation of ftsZ could be a major factor triggering the synchronized cell division of Prochlorococcus populations. This is the first application of quantitative reverse transcriptase-coupled real-time polymerase chain reaction (PCR) to natural populations of an environmentally relevant marine organism.