Seventeen years (1998–2014) of satellite-derived chlorophyll concentration (Chl) are used to analyse the seasonal and non-seasonal patterns of Chl variability and the long-term trends in phytoplankton phenology in the Mediterranean Sea. With marked regional variations, we observe that seasonality dominates variability representing up to 80% of total Chl variance in oceanic areas, whereas in shelf-sea regions high frequency variations may be dominant representing up to 49% of total Chl variance. Seasonal variations are typically characterized by a phytoplankton growing period occurring in spring and spanning on average 170 days in the western basin and 150 days in the eastern basin. The variations in peak Chl concentrations are higher in the western basin (0.88 ± 1.01 mg m−3) compared to the eastern basin (0.35 ± 1.36 mg m−3). Differences in the seasonal cycle of Chl are also observed between open ocean and coastal waters where more than one phytoplankton growing period are frequent (>0.8 probability). During the study period, on average in the western Mediterranean basin (based on significant trends observed over ~95% of the basin), we show a positive trend in Chl of +0.015 ± 0.016 mg m−3 decade−1, and an increase in the amplitude and duration of the phytoplankton growing period by +0.27 ± 0.29 mg m−3 decade−1 and +11 ± 7 days decade−1 respectively. Changes in Chl concentration in the eastern (and more oligotrophic) basin are generally low, with a trend of −0.004 ± 0.024 mg m−3 decade−1 on average (based on observed significant trends over ~70% of the basin). In this basin, the Chl peak has declined by −0.03 ± 0.08 mg m−3 decade−1 and the growing period duration has decreased by −12 ± 7 days decade−1. The trends in phytoplankton Chl and phenology, estimated in this study over the period 1998–2014, do not reveal significant overall decline/increase in Chl concentration or earlier/delayed timings of the seasonal peak on average over the entire Mediterranean Sea basin. However, we observed large regional variations, suggesting that the response of phytoplankton to environmental and climate forcing may be complex and regionally driven.