Emiliania huxleyi (Lohmann) W. W. Hay et H. Mohler is the most abundant marine unicellular coccolithophore in the ocean and belongs to the group of organisms that have chl c and fucoxanthins as pigments in the photosynthetic light-harvesting complexes (LHCs). In this study, we report on the isolation and characterization of the mRNAs encoding six light-harvesting complex fucoxanthin-binding proteins (LHCFs) from E. huxleyi. Phylogenetic analysis of these sequences has revealed that they form three distinct subgroups: haptophyte, diatom/haptophyte, and LI818-like. Expression analysis of the six Lhcf genes showed a clear down-regulation at the transcriptional level when the cultures were grown in high light (300 μmol · m−2 · s−1) when compared to equivalent samples in low light (30 μmol · m−2 · s−1). In contrast, little impact on transcript levels was observed between cultures grown in either low CO2 (180 ppm) or high CO2 (750 ppm) at either light intensities. Using polyclonal antibodies to three of the LHCFs revealed a down-regulation in protein levels in response to increased light availability with a minor increase in two of the LHCFs in elevated CO2. This study has provided an insight into the diversity of LHCFs and how changes in the levels of these proteins, together with altered pigment composition, may contribute to the flexible response of E. huxleyi to changes in the light environment.