Alterations in phytoplankton biomass, community structure and timing of their growth (phenology), are directly implicated in the carbon cycle and energy transfer to higher trophic levels of the marine food web. Due to the lack of long-term in situ datasets, there is very little information on phytoplankton seasonal succession in Cyprus (eastern Mediterranean Sea). On the other hand, satellite-derived measurements of ocean colour can only provide long-term time series of chlorophyll (an index of phytoplankton biomass) up to the first optical depth (surface waters). The coupling of both means of observations is essential for understanding phytoplankton dynamics and their response to environmental change. Here, we use 23 years of remotely sensed, regionally tuned ocean-colour observations, along with a unique time series of in situ phytoplankton pigment composition data, collected in coastal waters of Cyprus during 2016. The satellite observations show an initiation of phytoplankton growth period in November, a peak in February and termination in April, with an overall mean duration of ~4 months. An in-depth exploration of in situ total Chl-a concentration and phytoplankton pigments revealed that pico- and nano-plankton cells dominated the phytoplankton community. The growth peak in February was dominated by nanophytoplankton and potentially larger diatoms (pigments of 19’ hexanoyloxyfucoxanthin and fucoxanthin, respectively), in the 0–20 m layer. The highest total Chl-a concentration was recorded at a station off Akrotiri peninsula in the south, where strong coastal upwelling has been reported. Another station in the southern part, located next to a fish farm, showed a higher contribution of picophytoplankton during the most oligotrophic period (summer). Our results highlight the importance of using available in situ data coupled to ocean-colour remote sensing, for monitoring marine ecosystems in areas with limited in situ data availability.