Polycyclic aromatic hydrocarbons (PAHs) are widespread pollutants in marine ecosystems including threatened and potentially sensitive coral reefs. Lower organisms such as phytoplankton, known to bioconcentrate PAHs, could serve as potential entry points for these chemicals into higher trophic levels. Here, we present a novel method using a 13C-labelled PAH and cavity ring-down spectroscopy (CRDS) to investigate accumulation, uptake rates and trophic transfer of PAHs in corals, which are key organisms to sustain biodiversity in tropical seas. We quantified the accumulation of 13C-phenanthrene in the marine microalga Dunaliella salina, and in the coral Acropora millepora after diffusive uptake from seawater or dietary uptake via labelled D. salina. Additionally, we monitored the photophysiological health of D. salina and A. millepora during phenanthrene exposure by pulse-amplitude modulation (PAM) fluorometry. Dose-dependent accumulation of 13C-phenanthrene in the microalga showed a mean bioconcentration factor (BCF) of 2590 ± 787 L kg−1 dry weight. Corals accumulated phenanthrene from both exposure routes. While uptake of 13C-phenanthrene in corals was faster through aqueous exposure than dietary exposure, passive diffusion showed larger variability between individuals and both routes resulted in accumulation of similar concentrations of phenanthrene. The 13C-PAH labelling and analysis by CRDS proved to be a highly sensitive method. The use of stable isotopic label eliminated additional toxicity and risks by radioactive isotopic-labelling, and CRDS reduced the analytical complexity of PAH (less biomass, no extraction, fast analysis). The simultaneous, precise quantification of both carbon content and 13C/12C ratio (δ13C) enabled accurate determination of 13C-phenanthrene accumulation and uptake rate. This is the first study to provide empirical evidence for accumulation of phenanthrene in a phytoplankton-coral food chain.