Molecular techniques have revolutionised our ability to characterise plankton diversity but remain underutilised for generating climate relevant ecological indicators. Here, we calculated community temperature indices (CTI) for phytoplankton and copepod communities using long-term observations at Australia’s IMOS National Reference Stations using microscopy datasets and molecular datasets at both species-level and zOTU level, to evaluate how effectively each dataset type captures thermal tracking. Copepod derived CTIs showed strong and consistent alignment with sea surface temperature (SST), regardless of dataset type, demonstrating their robustness as method independent indicators of long-term ocean warming. In contrast, phytoplankton CTIs varied substantially among analytical approaches, with molecular methods detecting broader thermal spectra due to their ability to resolve cryptic and rare taxa generally overlooked by microscopy. Although molecular datasets operate with incomplete reference libraries, they retain sufficient ecological structure to generate interpretable thermal metrics, with sensitivity expected to improve as genomic resources expand. Divergent CTI estimates between molecular and microscopy datasets highlight methodological biases, particularly underdetection of cool water taxa in microscopy inflating warm water taxa observations. Our findings demonstrate the complementary value of molecular and traditional taxonomy and support the integration of molecular‑derived CTIs into global ocean observing systems as climate‑sensitive ecological indicators.