Phytoplankton community composition and its temporal dynamics were evaluated in the Alappuzha near shore waters (<15 m depth), including mud bank region, located along the southwest coast of India, using HPLC-derived marker pigments and microscope-based species composition data. The study has shown a characteristic phytoplankton succession pattern, wherein an exceptional increase in chlorophyll a (Chl a, >10 mg m−3), observed in the whole study region during the peak southwest monsoon (SWM - July) period, apparently unveiled the biological manifestation of nutrient enrichments facilitated by the coastal upwelling phenomenon. A conspicuous increase in fucoxanthin (a biomarker for diatoms) perceived across the study region clearly indicated the preponderance of diatoms (mainly Thalassiosira sp., Skeletonema costatum, Trieres mobiliensis, Nitzschia sp. etc.), particularly during the peak SWM period. The CHEMTAX calculations have shown the significant contribution of Chl a (av. 76% of total Chl a) from diatoms, regardless of seasons, compared to other taxonomic groups. Furthermore, the combined results of HPLC-CHEMTAX analyses have demonstrated the seasonal occurrence of various small-sized phytoplankton functional groups (PFGs), specifically cyanobacteria, cryptophytes and chlorophytes, along with the predominant large-sized PFGs, i.e. diatoms (mostly) and dinoflagellates. The relative increase in zeaxanthin prevalent during the warm periods (Pre-SWM and Post SWM) signified the presence of cyanobacteria. By contrast, during the SWM period, a conspicuous increase in Chl b and alloxanthin recorded in the whole study region indicated the abundance of green algae and cryptophytes, respectively. Likewise, a nominal increase in peridinin (a marker for dinoflagellates) prevalent during the onset of SWM was apparently due to the proliferation of dinoflagellates, Tripos furca and Prorocentrum micans (microscopically confirmed). Even though the overall CHEMTAX results clearly complemented the microscopy derived phytoplankton composition data, especially the abundance of large sized PFGs, (i.e. diatoms and dinoflagellates), this particular analysis could enable the portrayal of seasonal dynamics of small-sized PFGs (mainly cyanobacteria and cryptophytes) as well, as this information is highly significant as far as the study region is concerned.