<p>Phytoplankton biomarkers and functional group composition were characterized for the first time in the coral reef lagoons and adjacent open waters of the Lakshadweep Archipelago (LDA) during the winter monsoon of 2022, using a HPLC-CHEMTAX approach. The study area was characterized by warm (&gt;29 °C), oligotrophic surface waters throughout sampling period. Although chlorophyll <i>a</i> concentrations were uniformly low (mean 0.06 ± 0.05 mg m⁻³) with minimal spatial variability, the distribution of diagnostic pigments and corresponding phytoplankton functional groups (PFGs) exhibited distinct lagoon-specific signatures. Among the detected biomarkers, zeaxanthin, DV chlorophyll <i>a</i> and peridinin, were most prominent, albeit in low concentrations, indicating the relative dominance of cyanobacteria (<i>Synechococcus</i> and <i>Prochlorococcus</i>) and dinoflagellates, respectively. CHEMTAX-derived outputs provided the major PFGs and their proportional chl <i>a</i> contributions. The occasional presence of fucoxanthin, particularly in the Kavaratti, Bangaram and Agatti lagoons, suggested a sporadic occurence of diatoms. In contrast, cyanobacterial populations dominated the open waters and the Perumal Par lagoon, supported by both <i>Synechococcus</i> and <i>Prochlorococcus</i>. Photopigment-based indices, particularly PPC_TP and PSC_TP ratios, indicated an overarching dominance of smaller phytoplankton (&lt;2 µm) consistent with the oligotrophic nature of the lagoons. However, a marked increase in PSC_TP in the Kavaratti lagoon signaled a shift toward moderate productivity, likely associated with higher abundance of larger phytoplankton, predominantly autotrophic dinoflagellates and diatoms, and increased nutrient inputs, potentially reflecting rising anthropogenic pressures within in the lagoon.</p>